I think fanboys, whether it's for Marvel or DC, should be reminded of this regularly. I see way too much pissing contests on these boards.
To me, what matters the most is that the film I'm watching is great. I think Captain America: The First Avenger is a great film even though there is wasted potential in Red Skull. Is the generic villain a problem when the film as a whole is great? I'd definitely say that for the individual film, it's not. The problem for me arises when I think about the long run because eventually Marvel will run out of big screen potential villains and by that time it feels like a waste that they killed off Ronan, Red Skull, etc. But for the individual film, what matters is that the film as a whole is great. I think Marvel Studios has succeeded in creating great films despite mostly run-of-the-mill villains.
I think one reason for why most of the MCU villains aren't as great as Magneto, Loki etc. (won't even try to compare to Joker) is 1) lack of interesting presence, but also 2) less screen time.
When it comes to lack of screen time, it becomes a matter of priority, and then the question of whether or not there is a problem with their villains becomes a little more complex.
Would the Marvel Studios films be as successful if they gave their villains more screen time?
I'd argue that they'd not. Because a main reason for why their films are so great and successful is because they have such well developed and likeable heroes. And if you want to give the villains more screen time, you have to take from the heroes. Because seldom Marvel Studios waste screen time on other things. And thinking about that, I'm perfectly happy with how Marvel Studios' have handled their films, because I'd chose a well developed and prioritized super hero before the villain any day of the week.
That's not to say we can't have a bit of both, and I'm not saying Marvel Studios' handle this perfectly. Malekith could have been a lot better even with the little screen time he had. Same goes for the likes of Mandarin, Ronan, Whiplash and so on. But not everything is perfect and sometimes we have to appreciate things that are great but not perfect. I mean, it's one thing to give contructive criticism about certain aspects of films, but I think it's an exaggeration to call the villain case a serious problem. At least for the individual films.