No secret identities; empowered women; lame villains (except Loki!); more tell-tale signs
It might sound strange to say about a series that has produced some of the most popular superhero films ever, but a Marvel Studios film doesn't spend much time having fun with superpowers. Thor can control the weather, but he mostly hits people with his hammer and because the Thor films toss out the idea of a human alter ego, they also prune out some of Mjolnir's more outlandish transformative enchantments. (It's basically Boomerang Excalibur.) The third Iron Man film had a lot of fun with Tony's new remote suit, but it also sent the hero on an armor-free mission, the equivalent of one of those 007 movies where Bond goes on the run. Pretty much every Marvel movie comes down to a slugfest between two human beings with roughly equal superstrength, although sometimes it comes down to a bad guy firing some really powerful ray at the good guy.
Supervillains who in comic book form had highly specific superpowers usually get depowered (bye-bye, Mandarin's Rings!) or granted a myriad assortment of super-skills (see: Loki's skill-set grab bag: Telekinesis, telepathic projection, semi-invulnerability…or just see all the Asgardians). More generally, the Marvel Studios films take place in a world where superpowers are often quite tenuous. In The Avengers, Loki uses the Tesseract to mind-control several S.H.I.E.L.D. agents, and Hawkeye gets cured of mind control via excessive punching.
This marks a notable contrast to the other major Marvel superhero franchises, like Spider-Man, where barely two seconds pass without the character climbing up a building or throwing webbing at someone, or X-Men, the later films of which feel a bit like The Wacky Superpower Variety Hour. Cynically, you might suspect that the lack of emphasis on specific superpowers is partially because of those other franchises. The Marvel Cinematic Universe is a universe assembled out of financial necessity: The studio doesn't own the X-Men, which means it also doesn't really own the concept of mutants, which means that Agents of S.H.I.E.L.D. has to carefully tiptoe around the notion of superpowered people emerging everywhere. (Also problematic: With an estimated twenty kamillion characters, the X-Men may have stolen all the good powers and most of the bad ones, too.)
Less cynically, you might point out that Marvel Studios started making superhero movies almost a decade into the superhero-movie era: The point at which everyone had seen a man fly (or web-swing) for a long time. The company's films spend more time on character-building than on power-demonstrating. Most of the best bits in Avengers are just long dialogue scenes between the characters, which is not something you can say about Man of Steel.
Image Credit: Zade Rosenthal/Marvel Studios