To me, the recognition of an actual fault is specific, I can point to exactly what is wrong and state exactly why it is wrong. While self-doubt, for me, is generally vague. e.g. What if this is like a hundred other stories? Are my turning points too weak, maybe not justified enough? Should I cut the sex scenes to be suitable for a younger audience?
If you can Google for fixes to your perceived problem and find something more than generalities and platitudes, you can see if those fixes apply to your situation.
In your specific case, thinking the plot is done to death: Who exactly do you think has done this plot? If it "unoriginal" and done to death, who has recently failed with this plot? Where have you seen it and been bored?
You might be right, but also remember a huge percentage of best-sellers follow the beats of a 3 act structure, because it works. It is possible your concept is unoriginal, but still works! (Look at Romances, for example). In such cases, the value is all in the execution, the details of the characters, their situation, and their personalities.
Take for example "The Truth About Cats and Dogs", a Janeane Garofolo movie 1998 I think). It's a fairly standard romantic comedy (it wouldn't work in the modern world due to the Internet, but neither would You've Got Mail or Sleepless in Seattle), nevertheless at the time it was hilarious because of the execution alone, including the cast. I recognized every standard beat in the movie, but I loved it anyway. Just because, while watching, I am thinking "complication goes here", and turn out to be right, doesn't mean I can't be delighted by the imagination of the writer.
(My family says I'm not allowed to comment on movie structure when watching movies. Too many spoilers.)
Plenty of best sellers follow the Hero's Journey practically to the letter, and it is just an expansion of the 3AS. Because it works, people like stories structured like that. A lot of people forget that Joseph Campbell synthesized the Hero's Journey as a generalization of hundreds of beloved myths in cultures all over the world. It isn't a prescription for a story structure, it is a description of the story structure of memorable, beloved stories.
So are you really certain it is a bad thing? Isn't your execution at least original? Your characters, or setting, or the complications? Because maybe it is "done to death" for the same reason the Hero's Journey is done to death, because with a little originality, it is evergreen. It keeps working because it taps into the very psychology of what people think is a good story.
If you have a real fault, you should be able to identify it analytically, more precisely than "I just have a feeling". If you make an effort to do that and the only way you can articulate the perceived fault is in vague terms that suggest no course of corrective action, then I would call that self doubt.
Accept your self doubt, and proceed anyway.