Do too many scenes exhaust the reader?

Perhaps you've guessed this may be another form of "Kill your darlings"

I wonder if it may be the "add to the character's development/ lay the groundwork but doesn't add up to the current plot" scenes are the ones making the story hard to read for your audience?

Look into your story's theme. (using the present story as the first focus then the series plot.)

I might be facing this with my story (series) too. It is really difficult to narrow down a series worth of events into a single book (at least I am finding.) So much so, I wrote a lot of short rough drafts, taken several turns and a few rewrites. I have a similar type process (Part plotter, and part pantser) I have a general grand scale plot mapped out. There are certain key plot points that must happen. How those happen is a bit less organized. I let the characters figure out how to get there. (usually by imagining the scenes first before writing.) Sometimes I have to force the characters along and sometimes they surprise me with better ideas that totally mess up the story or even a section of the series. The detours may be annoying, to the point I may try everything I can do to resist it, but in the end it seems the characters know best, and it is better to go ahead and rewrite if needed.

That said, you may have to trim/ narrow down/ remove the scenes that don't add to the plot. If they are critical to the series, then they also have to be reworked to fit the theme of the current story as well.

I found this article very timely as I was struggling with a scene between two of my characters that needed to happen. What I wanted them to talk about was not important to the current story's plot, so in the end I had to scrap it and have them talk about about something more relevant to the current story. (yes there's a murder in their back story and things that if revealed will rekindle old hate and more drama, but since book 1's theme is not about the murder event, that whole subplot can't be included in book 1 (It does loosely fit the theme about overcoming bullies, fears, regrets, but does not fit because the book's plot that is focused on the two former friends turned enemies coming to face with each other resolving their emotions relating to a different life event.) Stuff about the murder would be interesting, but would skew the plot of book 1 and make it hard to read.

What I did is drop little hints referring to it, but downplayed the impact/ foreshadowing and played up the part of getting the two characters to come on friendly terms. That way I hopefully set up the groundwork that will give a satisfying ending (seeing the two friends together) but also a question in the reader's minds learning that things could drive them apart later.

That said, I'm far from finished and sure I'll have to sort through more stuff in the next draft. I may also have to accept there may be parallel novels related to the same time span, but relating to different characters, since some of their stories have a completely different goal than the other character(s). Enough that I can't force it into being a side plot.

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Rereading your post, perhaps my answer may not be that helpful after all, but it still sounds like a "kill your darlings" situation.

Repetitive scenes - Pick the one you like the most/ that works the best for the plot. The others may have to go (unless they give new plot stuff, then focus on the new stuff for the next version)

Lack of transition: I struggle with this too. Sometimes it is simple as looking over the dialogue scenes. Did any of the characters jump to the next topic without reacting?
(This is feedback I got on my story from readers.) I found sometimes going back and reworking on it changes the whole nature of the scene, but in the end makes more sense. Even if it means I can't keep any material from the old draft. Sometimes doing this cuts down on the repetition. (I find since the topic already got addressed and the appropriate emotional response met, then the other scenes trying to bring that characters emotions aren't needed.

What are various ways to reduce reader fatigue by adjusting scenes?

1. Make sure there is a point to the scene. Does the POV character have a goal? If not, consider adding one. A scene with a goal will give the reader something to look forward to. Will the character achieve the goal?
2. Make sure there is action. What action does the character take to achieve the goal? If there is action, the reader is more likely to feel that there is momentum, that the story is going somewhere.
3. Make sure there is a disaster or obstacle that keeps the character from reaching the goal, or a new complication that develops as a result of achieving the goal. These disasters string scenes together and give them continuity, if done right, in that one disaster leads to the next goal, which then leads to the next disaster and so on until the character finally gets it all figured out or dies trying by the end of the book. In addition to a sense of continuity, disasters also give the reader a sense of conflict and stakes. Story is conflict, and the disaster in each scene is where the story lies. No conflict, no story, bored reader.
4. Include a reaction. From a single phrase in which the character winces, to pages of internal monologue, give the reader a chance to see that the character is a human (or human-like) being by showing a human reaction to the disaster. Reaction is where the reader is going to develop empathy for the character, and if the reader has no reason to empathize with the character, then the reader has no reason to care about the character or the story.
5. Include a debate. This one should probably be used with great subtlety, but after the reaction, give the character a little space to plan on what to do next. This step should probably even be skipped altogether in tense, action-driven stories in which there is a lot of gut reaction, but the reader would probably grow weary of constant in-your-face action. Occasionally, give the character space to breathe and plan in order to give the reader space to breathe and think and see the character once again behave like a person in order to create empathy.
6. Include a decision. Let the character come to a decision on what is to be done next. This leads into the next scene, as this scene's decision become the next scene's goal. Again, this gives the reader a sense of continuity and flow.
7. Cut everything that doesn't belong in the above. The time readers have for reading is growing forever shorter due to other things demanding attention like video games and Facebook and Stack Exchange. Honor the time readers are giving you by not wasting their time. Make sure every sentence in every scene is pulling its weight. If it isn't supporting scene structure, then it's probably there for the author's benefit and not the reader's. Cut it and shorten the scene.
8. Include variation. Between the shorty-shorts and the chapter-long scenes, it sounds like you got this covered, but keep tense scenes short, and let internal, character-heavy scenes linger a bit. Mix them up, but arrange them so that there is rising action throughout the book that climaxes at the... well, the climax.

Obviously this is 100% my opinion, there is no hard and fast rule. Consider how many scenes are in King's epic book The Stand: I bought it when it first came out and I couldn't put it down. What is that thing, half a billion words? Actually 472,376. ONE NOVEL (and importantly, a recent, modern, best-selling one).

So I certainly don't think too many scenes exhaust the reader. If the reader is exhausted it is (IMO) because the value-vs-work ratio is not in their favor.

Meaning, they have to do too much mental work (remembering facts or characters, backtracking, recalling too many unresolved threads or puzzles, they are expected to intuit too much) to understand what is going on, so their enjoyment of the story is diminished to the point they put the book down.

Have all the scenes you want! You just have to keep things simple, do not take to heart the aphorism of "weaving plot lines". They are all nice simple arcs stacked in neat rows, side by side.

Your story cannot be hard to follow.

YES, scenes should flow seamlessly. Abrupt scene changes are not necessary and do not add to the "surprise". A scene ends when (and only when) it is clear to the reader that whatever was happening is now concluded and something else is going to happen now. Hopefully the reader is looking forward to that, because they want to see what it is, or they know what it is and want to experience it (something dramatic is about to happen).

Thus if a scene ends "abruptly" the reader feels cheated, something was left out, you have a ragged end and hanging threads. Of course if the scene has "ended" naturally (Harry Potter finishes his countdown to midnight so he is officially eleven years old), and the reader really expects nothing else, then your transition (and semi-cliffhanger) can have its few lines: A deafening series of knocks on the door shakes the house! BOOM BOOM BOOM. (Hagrid has arrived, the next chapter ensues).

But Harry's little countdown is over, no drama is interrupted, nothing is unresolved in that scene, and in that sense, this transition is seamless.

A flashback is not forbidden, but remember that the reader has to memorize the current 'state' of the story, the setting, the characters, what is happening, what is about to happen. Then they have to hold that while they start a parallel and different story, the flashback. New setting, characters, series of events, and at the end recall all the first setting characters, events so far. That is a lot of mental work. You should be judicious in making the reader do this much work, flashbacks are tiring.

Simple memories are not flashbacks and not "a scene" and not tiring, "It reminded him of being hit by car, riding his bike at eleven. Ever since, he'd been terrified of red Hondas."

If you feel you need to use flashbacks (fleshed out scenes that interrupt other scenes) I'd suggest making the scene interrupted very simple (not hard to recall who was there and what is going on), and perhaps still return after the flashback with reminders of the current state in that scene.

Your ideas of improving transitions and seamless endings are good.

I would also suggest that when one scene ends (for some POV) then at least the setting of the next scene for that POV should be clear to the reader, or something about it at least: Who they are meeting, where they are going, what they must find.

Minor exceptions are alright: I have characters in city A, their scene ends when they step on the road to town B. The next scene for them begins like

They were still five miles from B, and John was explaining to Mike the proper brewing of hard apple cider.
Mike interrupted him, and stopped walking.
"Stop." He turned his ear down the road. John looked but saw nothing but the bend ahead, still he knew better than to speak.
"Company coming," Mike said. "More than two. Three or four, I can't tell."
John said, "That cove we passed a few minutes ago is defensible. Should we run for it?"

The continuity and connection still exists: The reader expects B, they are nearly there. So this scene is a surprise but a plausible one; you are walking somewhere and an event occurs. They may still get to B, or not: if in this scene they discovered something from the people they meet (say Town B is completely destroyed, there is only dirt left), then they will likely have a new destination. That is okay, we provided continuity and the reader is not confused about what is going on.

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Added to clarify question by OP in comments:

OP: John's final line in your example strikes me as a similarly simple transition. If you had left it out, and they were then at the cove, it would be a new scene, yes?

Me: John's final line would be a good transition, to a new scene in the cove. I would probably add one more: "They turned and ran for it." or something like that.

However, If you left it out, and suddenly they are in a cove, that is a new scene but an awful jump cut. Cuz, what? A cove? What cove? Who decided that what Mike heard was not "company" but a threat? Why?

That jump cut is not fun drama, it asks the reader to do too much work and work is not fun. It is a pothole in the story. Also, it makes the cove a D.E.M., too magically convenient.

However, an adventurer and/or soldier silently noting defensible formations as he walks --- okay, that's plausible.

Although much of writing is indeed aiming to create lasting questions in the reader's mind (how will they succeed against these odds, what will the villains do next? In the snippet above, what is the clue Mike will find in B? Will there be a clue, or is it a dead end, and if it is, what does Mike do next?

Those are good questions to try and get into a reader's mind, but we don't want just ANY questions. Specifically, as related to Scenes in this question, we never want a reader to have questions about what happened between Scene X and Scene X+1.

So it is true, Mike and John leave A, and are on the road to B, and we missed maybe two days of that walk. What did they talk about? Since we did not show that, the reader assumes it was nothing important, like the snippet I gave, "the proper brewing of hard cider". As an author I must honor that expectation, I cannot come back three chapters later and say that during this walk John taught the bookish Mike how to do a Muay Thai Sweep which was a key martial arts move in the plot. If that happened, it must be not only motivated but shown.

So the reader assumes "things" happened on the road for two days, and may wonder what in the world they talked about.

I don't have to describe Mike and John running for the cove if nothing important happens during that run, or the hiding, or waiting. The next scene would start at the tail end of those non-eventful minutes, for transition sake we cover those in a sentence, then something eventful happens. Perhaps first sight of the strangers. Perhaps somebody coming from the other direction. Perhaps Mike no longer hears them and John gets bored waiting, and makes a decision to go investigate if the strangers are hiding, in ambush or in fear.

But to sustain continuity, the reader should never be jerked out of the story by a WTF moment, wondering if somehow a paragraph went missing, or having to read the last few paragraphs with closer attention to figure out what must have happened. That kind of question, by the 2nd or 3rd instance, can be a story killer. It is the author's job to not bore the reader with descriptions of the 100% predictable and mundane, like walking, or driving, or sleeping, or routine work, or routine sex for that matter. For continuity such things are noted and discarded.

But it is also the author's job to understand the reader is (hopefully) immersed inside the story, as one of the characters, so every important thing said or action taken or set decoration seen or heard or felt (cold, heat, wet, parched) should be described, or the reader gets jerked out of the story in order to rationally analyze the story, because her camera (the narrator) is on the blink and she missed something.

What is important? Anything that matters, which means anything that will influence something that happens later in the story.

To be clear, you do not have to write exclusively about important things. John's average appearance may not play any part in what John does, or make any significant difference in the story (other than he is not treated as unusually tall, short, heavy or thin, but that is the reader's default assumption anyway). Still if you think appearance descriptions are crucial, go for it. Mike can admire the landscape, mountains and rivers he has never seen before, but they don't have to matter or play any part later, they don't have to present either obstacle or opportunity or be considered in strategy. They can just be a placid river, or a mountain with a cloud at its peak, that to Mike's amusement looks like the mountain is wearing a fluffy white sombrero, to help the reader's immersion into the mood and setting. Such description is part of writing too, sometimes very enjoyable to us readers. But note that if we left it out the reader wouldn't really miss it, if anything they would just assume that the landscape is average, boring, and not important to the story.