4. Blame The Avengers
Unfortunately, it was Phase 2 which really cemented the idea that there was a villain problem, and there’s only one movie to blame: The Avengers. No, it’s not that Loki was bad - in fact, his turn in that team-up movie made him one of Marvel’s biggest characters - it was that Joss Whedon's flick changed the focus of MCU movies entirely.
Until then the films were surprisingly small-scale affairs; there was spectacle, yes, but heroes were only really going up against small teams of enemies and usually one villain. The Avengers, on the other hand, needed a threat big enough to warrant seven different superheroes teaming up, so the director had them fight a literal army.
It made for easily the best third act Marvel had put together at the time, but it set the bar in terms of scale that every subsequent movie had to follow. It was no longer enough for the stakes to be personal, the entire world had to be hanging in the balance, with the villain hidden behind waves of interchangeable henchmen. This made for a sense of spectacle that other franchises - like Fox with X-Men: Apocalypse - immediately attempted to ape, but it meant that main villains were pushed aside even more in favour of focusing on battles which didn’t even feature them.