You don't want to think like just any old supervillain. Most of them have systematic flaws in their behavior too. Besides the obvious, in a lot of stories the motive that best explains the villains' behavior is not really to succeed but the one the author has for them, which is to put up a good fight and be awesome, but lose. If you try to be like them, you might end up just trying to try. Your mind will censor out the non-grandiose but effective plans. You do not want to be about demonstrating a good effort. You want to be a winner.

Edit: the next paragraph has spoilers in it for Watchmen. So does the single line after it.

If there's one supervillain people should maybe try to emulate, it's this guy. He defeats an invincible character, stronger than Superman in a world where no one else has significant super powers, with nothing but mind games, (and in the movie at least), nukes several cities and blames it on said godlike character (the comic book ending has him blaming it on aliens, I like the movie ending better), tricks the US and USSR into thinking they have a common enemy, and prevents a larger nuclear war. He exemplifies the utilitarian answer to the trolley problem you mentioned. He's totally ruthless, but for a just cause. And most importantly, he wins.

But don't try a plan that risky in real life. You're not a comic book villain and it probably won't work out.

Opportunities to kill a whole bunch of people, and actually accomplish more good than you could through alternative methods are rare. If you want to be awesome (virtue ethics), try to make yourself into the kind of badass consequentialist who could do that in the rare circumstance when it was a good idea. If you want good to win (genuine consequentialism) optimize your mind to correctly deal with the choices you encounter in real life, not the ones people deal with in cool stories.