Though he still managed to manipulate the Avengers against each other before they rallied together for the grand finale.
It could also be said that the Tesseract was driving him crazy and causing him to be power hungry at the expense of long term planning.
He's back to his old self in Thor 2.
In Home Alone 2 Marv is a lot dumber than in the first film, possibly thanks to the head injuries he sustained in the first film (and/or additional head injuries he might have sustained in prison).
Idiocracy: This trope happening to the entire human race is basically the plot.
The Mask has both a film-wise and adaptation wise example for Lt. Kellaway's partner, Det. Doyle. In his initial scene at the bank, Doyle seems to be quite intelligent. By the time we see him at the park, he's suddenly a ditz and by the film's end he's a certified idiot (though some of that may have been him being influenced by the Mask's power). The cartoon made him even dumber.
The Neverending Story III: Falkor, who is supposed to be a very smart character. He is a smart character in the first film and still somewhat smart in the second. In the third, however, he becomes a downright moron.
In Raiders of the Lost Ark, Marcus Brody was portrayed as a highly intelligent, very serious character. When he shows up again in Indiana Jones and the Last Crusade he was suddenly an incompetent load who couldn't even initially tell that he was being kidnapped... even as Sallah was screaming at him that the bad guys were doing exactly that.
Chief Inspector Jacques Clouseau from The Pink Panther. In the first film, he was actually a bit intelligent, if a little clumsy. It wasn't really until his second film, A Shot in the Dark, that he became the bumbling detective that we all know and love. Surprisingly, his animated counterpart is far more competent, although he makes up for it by having a lower success rate for solving crimes.