Misunderstood? Yes. A lot of his movies are better than the critical assessment. Part of the difference, I argue, is due to his different storytelling preferences, he doesn't go for happy endings for example, there's always a cost and that's not something people want to see.
Genius? No. Geniuses are rare and people throw that term around too often. It depends on your definition of genius, mine would be one who introduces new ideas, new concepts, new methods that are very good ideas, concepts, and methods. Snyder might a genius for visuals, but that's not what this discussion is about. The only geniuses in CBMs right now or even recently are possibly:
- Christopher Nolan, has made the best movies, and they were a break from what came before. He successfully placed the hero in a contemporary, ordinary world, he also went for a serious tone with high suspense ;
- Joss Whedon, has the best writing track record of them all if you include Buffy, Angel, and Firefly which I do. He has the first female action protagonist (through Buffy) that was popular and of a different style from the Ripley/Connor archetype that is still the most common. The Avengers is the first team-up movie to work and was previously thought to be impossible. X-Men were not true ensemble films and Fantastic Four was not well-regarded;
- Alan Moore and Frank Miller were geniuses in the 1980s;
James Gunn, the Russo Brothers, Matthew Vaughn, Zack Snyder, Jon Favreau, Bryan Singer, etc. are merely competent. They apply a lot of ideas that have already been introduced to the popular consciousness and oftentimes they apply them well. However, I'm not convinced that they create/introduce any new ideas effectively, and even if they do, those are few and far between.