The best rule I ever read for making a villain is to treat your villain as the most important character in your story and make him/her the most interesting character, even more so than the hero. As alluded to in @Rasdashan's answer, one of the most discussed villains right now is Thanos from the Avengers movies, who has a similiar goal in solving the world's problems by a universe level cull of the population, thus solving the Overpopulation problem. What makes him interesting is that he actually does care about the people he's willing to kill... which is why it's a coin flip... so that he's not doing it out of malice or spite or love or affection, each person is given a 50:50 chance to live or die... if a sinner lives and saint dies, so be it. He's not going to use any system of evaluation other than random chance to determine this. This alone qualifies him as "Not as big of a jerk as you could have been award." What really pushes him into sympathetic territory is that he has children that he deeply loves and are all adopted. Even if they don't return his love for them, he never stops loving them... and in one of his final acts in the film, the fact that all but one of his six children are now dead, it allows him to commiserate with a hero who has just lost someone she loves... and he also tearfully admits that to him, the personal nature of his loss... is still worth it to him... which is the gut punch to the audience... It also sets up a major theme of the film... As Captain America points out when the simple solution to the threat of Thanos is the death of one character on his team, "we don't trade lives." Meanwhile, while never echoed by Thanos, he does exactly that because it is a simple solution.
When writing a villain, the best ones will never see themselves as the villain... they think they are the hero... that whatever they do, they're actions are justified for the greater good of the mission. At least in their own mind.
A cull would be a logical solution to overpopulation, but not an ethical one... to most people... to most people... but what is logical is not ethical and what is ethical is not logical. The best villains will make the hero counterpart question if they did the right thing in opposing him... and he might not like what the answer says about himself.
To look at another franchise, X-Men, the main villain, Magneto, is often one of the most beloved villains in all of superhero works... because he and his opposite number, Charlse Xavier, both have the same goal (Mutant safety and acceptance) but go about it in different ways that are unrecognizable (Often summed up in saying Magneto is Malcolm X to Xavier's Martin Luthor King Jr.) and they actually are good friends and Magneto will admit that Charles has some good ideas but he's seen a history that disputes the work-ability of them.
Magneto grew up a Polish Jew during the Nazi Occupation. His life was threatened once because of the circumstances of his birth and he does not want to be in that situation ever again. Xavier was never a victim in the same way Magneto was and believes that most people are better than the Nazis. Magneto has no tolerance for bigotry and will oppose it, viololently if necessary... Xavier believes that this only creates a circle and sees it more productive to show the world the good mutants can do. They can agree on goals, but not solutions to achieve these goals. The final conversation of the first film sums up the relationship perefectly. With Magneto in jail, Xavier goes to visit his friend and they have the following discussion:
Magneto: Doesn't it ever wake you in the middle of the night? The feeling that someday they will pass that foolish law, or one just like it, and come for you and your children?
Professor Xavier: It does, indeed.
Magneto: What do you do when you wake up to that?
Professor Xavier: I feel a great swell of pity for the poor soul who comes to that school looking for trouble.
It's here where Magneto realizes where he's wrong. Charles does not give up on the goodness of people, and feels that if he can show the world that mutants who can control their powers and understand how they work and use them for the defense of others, humans or mutants, then he can show mutants to be worthy of judgement on the content of their character, not their content of their genes... and if still they insist on starting a war, they know the enemy will be capable of defending themselves.