I'd say Marvel does have a villain problem, but they've had some solid ones that I think people forget about. Kurt Russel was great as Ego and rewatching The Winter Soldier, Robert Redford is pretty good as the villain. The latter is easier to forget since he's a pretty human villain with not a lot of flash and is pretty toned down. It's also perfect casting, taking a guy who starred in Three Days of the Condor, one of the political conspiracy thrillers that inspired. Anyway, I think the villain thing is a problem Marvel is overcoming but thinking back on it, I think there are more solid villains than people remember (in my opinion). It's just that too many, sadly, are just plot advancers, like Ronan and Malekith (the latter probably being the biggest offender and a big waste of Christopher Eccelston).
But yeah, for one's I think are on the better end (that aren't Loki, obviously), you have Obediah Stane, Justin Hammer (granted, more for comedy value, since he's comically inept as a foil for Stark), Red Skull (sure, it's broad and cartoonish, but it's perfect for the movie's retro tone), Ultron, and the aforementioned Ego and Alexander Pierce (though I can easily see people disagreeing with me on that one). I'll also admit I might be a bit more generous with some simply because they aren't as bland as the others so far.
I will also say that Mad Mikkelson's is fairly forgettable but I think the actor gooses the character a little to make him slightly better. I really need to get around to Hannibal.