To answer the question, yes, I think Marvel does have a problem with its villains.
IMO, the only really good ones have been Kingpin and Loki, and even the latter's charm has been starting to wear a bit thin. Alexander Pierce and The Winter Solider were decent. The rest are just bleh (I haven't watched Agents of S.H.I.E.L.D. thoroughly yet, so I may be missing some).
I think that part of the reason that there is so much criticism of the MCU villains is because in the source material that inspired these movies many of them are very fleshed out and compelling. And even if they weren't originally, a talented writer and director can make them into something memorable.
Now I normally don't concern myself to heavily with the opinions of celebrities, but Marvel would do well to heed the advice of George R.R. Martin, because that man knows how to create awesome villains. Norman Osborne (should he appear in these films) should be the Tywin Lannister of the MCU; a truly horrible prick who uses his wealth and influence for his own gain, is willing to screw people over without a moment's hesitation, and is also a terrible and abusive father, as well as having a great presence (though a lot of that has to do with Charles Dance). And we should see all of this, which is another thing. I feel it would serve to improve these villains if we could get better insight into their characters.
And can I say it really bothers me how some people so readily sweep this issue under the rug and try to redirect this issue to other films? It goes to show a lot of insecurity on their part and unwillingness to discuss the issue. There is absolutely nothing wrong with demanding better things from a company, even if it's just a certain element.