I don't get the main villain's motives at all.

First time seeing it in theaters, I thought the same thing as you did.

Second time viewing at home with subtitles? His motivations became more clear.

Edison basically felt like he was abandoned after the War ended. As a war hero, he expected to make made a much higher rank and hold authority to others but instead, the higher ups gave him a ship and made him captain.. basically "War has ended, we don't need you anymore, here's a ship, see ya!".

After the USS Franklin went down, no help came either. Strike two. With no help from the Federation, they were on there own until Edison discovered the people there can prolong life. So he learned how to do it and the remaining crew prolonged their life.

Then after that, they planned their revenage against the Federation for failing them. Until Kirk's crew came a century later...

There seem to be more and more of these types of villains (who believe they are somehow doing good by killing and destroying). Liam Neeson in the Nolon Batman, for instance. I thought he was rather nonsensical, but I feel like I've seen this motivation reiterated repeatedly in the past decade or so.

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Edison was originally a soldier who fought in wars against alien races, Edison lived during the time when the relationship between humans and aliens was very hostile and strained and humans were constantly fighting in wars with various alien races for survival, and when humans were taught that fear and conflict made humans stronger. But then suddenly the military organization that he was enlisted in got dissolved and the Federation/Starfleet was created. Unlike the military, The Federation's objective was completely different to what Edison had been taught, instead of using conflict as the solution to solve problems, The Federation strive for peace and unity with alien races and believe that humanity as a race must evolve and change and be more open-minded and progressive in order to survive among other alien races in the vast universe, the Federation is an organization that believed in peace, unity, progression, inclusion, diversity and change, and believe that humans should establish civil and peaceful diplomatic connections with the different alien races and work alongside aliens to achieve the same goals, instead of fighting them. And because of the Federation's existence and teachings, humanity's opinions and attitudes towards aliens began to change and evolve and humans as a species became more open-minded about aliens. The Federation's objective and beliefs of peace and unity was completely the opposite to what Edison was taught and believed in and fought for, and that was one of the main sources for his resentment towards the Federation/Starfleet. I think being abandoned by Starfleet on that unknown planet only worsened Edison's views about the Federation, and as time passed his resentment and hatred towards them and towards humanity as a whole became increasingly bad to the point that he completely abandoned and betrayed his own kind and became the scorned and vengeful being that was Krall. But I don't think Krall/Edison was simply out for revenge, to Krall, he believed that the Federation/Starfleet had "corrupted" the human race with views of peace and unity and progression, so he set out to destroy the Federation and "eradicate" or "reset" humanity in order to start over with a clean slate.

But what I am confused about is whether Edison was originally forced to join the Federation/Starfleet, or he willingly chose to join the organization, I don't think that was clarified in the movie. If he had chosen to join Starfleet himself, then his resentment towards the Federation/Starfleet would not make much sense, because he should've known what the Federation's objectives are upon joining, if he knew that the Federation's objectives, beliefs and values were completely different to what Edison had believed in, then he wouldn't have joined Starfleet to begin with. But if he was forced to join Starfleet against his own will, then that would make more sense. I wish they had clarified this in the movie about whether Edison joined Starfleet willingly or not.

And let's not forget that it has been about 100 years since Edison/Krall and his crew were stranded on that planet, so maybe back then he and his crew probably only had limited resources on the planet, his ship the USS Franklin was inoperable, and there probably wasn't any other ships on the planet at the time so he and his crew couldn't leave the planet. I think he only gradually managed to collect more resources and built more ships as more time passed, but by then Edison/Krall's resentment and hatred towards the Federation had become so great that he was hellbent on revenge. But he needed that powerful ancient weapon in order to destroy Yorktown and get his revenge on the Federation. So he waited until the Enterprise crew found that ancient artifact which was part of the weapon he needed before he set his revenge attack into motion.

I think the contrast between Edison/Krall's beliefs and the Federation's beliefs and objectives mirrors our own society in reality quite well. I mean, even now our society is still quite divided in general, we have some people in this world who are more right-wing and still have more conservative and traditional views and opinions, on the other hand we also have people who are more left-wing and have more open-minded views and opinions and are more accepting of change and progression.