I've always thought of the Marvel movies as being based more on the Ultimates Universe. Why else would they have Samuel L Jackson as Nick Fury?
There are strong ties to both Marvel Universes...
Iron Man's movie origin is absolutely nothing like the Ultimate origin.
Cap's story is similar no matter which story you read - but, the U-Cap is a cocky arrogant SOB.
Movie Thor isn't a whole lot like either comic Thor. The lack of Donald Blake has ties to U-Thor - but, there's not a whole lot else that really that I feel links the two.
The Hulk storlyline started The Ultimates when Banner injected himself with the Super Soldier serum and the heroes unite to stop him. Banner was already working with SHIELD... and from what we've seen so far, Banner is already the Hulk and he's recruited by the Black Widow.
...and well, Sam Jackson is U-Nick Fury. No if's and's or but's about it. He is the most obvious and biggest tie to the Marvel Ultimate Universe.
So, yeah... I think the movie guys are picking and choosing what they want to use and making quite a bit of it up as they go. It would seem if the Chitauri are the Avengers villians that Joss and his group of merry Marvel moviemakers are taking liberally from the Ultimate Universe.
But, I think the Marvel Movie Universe is it's own very unique thing with strong ties to both Marvel comic book worlds.
All that said, I think I want to be avoid more direct spoilers... so I might not read this thread again until May 5 or 6.