If you mean the movies, their worst problem is that they're bland. Almost all of them are good, but very few of them are anything special. This is mostly due to lackluster color keying and uninspiring soundtracks. And they tend to not put much thought into their villains.
This leads to a universe of films that certainly feel like they all take place in the same universe, but not a very spectacular one. Basically the marvel movies are good, but they're missing that little spark that'd make them GREAT.
If you mean the comics, they're using gimmicky shticks to artificially inflate sales numbers, without attempting to tell genuinely engaging stories. And the few writers that ARE trying to just tell a good story keep getting shanghaied by endless events, de-railing what would've been otherwise good comics.
There's some good comics out right now, but they're constantly being hamstrung by larger company-wide events.