I have a few, but I think that the two obvious ones would be Hank and The Scarlet Witch. For Hank, he just can't seem to ever live down that pimpslap. And then we have his mental health issues and his breakdowns, and whenever he seems to be getting past that, some future writer always goes back to that stuff again with him. And now he's, Ultron? Evil? Dead? With Wanda, well, she's been turned into a villain twice, and then there is the whole House Of M thing. In addition to those two, I think that the Grim Reaper is a bit of a mess, too. He used to be a very big villain back in the day, and he used to be really cool, but his characterization has been all over the place for about a decade or two. Sometimes he's not really much of a villain, other times he has a stone-cold hatred of the Avengers and of his brother. I also think that he keeps on dying and coming back waaaaaaayyy too much! Maybe they just don't know what to do with him anymore. I guess maybe Dr. Druid has gotten a bad deal, to be honest though, I don't really care for the character. Tiara as well, she seems to have had some bad characterization. I can't think of any more off the too of my head, but what do you guys think?
I'm hard pressed to think of a character that hasn't suffered poor treatment in this century.
Somewhere along the line, they've lost the 'Marvel Method' of writing characters.
Stan and co. GAVE their characters problems.
The last few regimes at Marvel seem to see the characters AS the problem.