Hey, been following these forums for a while and decided to finally join and post my two-cents
Whedon has previously stated that he will be taking plot elements from the original 616 main Marvel universe and other stories(ala Ultimates universe) and from guesswork and common sense, it only makes sense the skrulls are going to be in the Avengers for a number of reasons:
1. Its obvious we need a threat big enough to bring Cap, Iron Man, Thor, Hulk, Shield etc. together and a massive alien invasion would warrant that. Alien invasion films have been done countless times but never have we need a "superhero alien invasion film" and as a poster mentioned, this could slightly tie into Iron man 3(with the mandarin's ring's possibly being alien technology from a crashed skrull ship that is reverese engineered by the Mandarin to create his rings)
2. An alien invasion by the skrulls would force the team to work together and would make for great character conflict and drama. I mean it would be cool to see Captain America and Tony Stark clash over tactics and ideals. Hawkeye and Black widow's romance in the face of an alien invasion. Thor unwillingly to work with anyone. Bruce Banner struggling to control Hulk to aid the avengers etc.
3.I think the Loki controlling Hulk storyline will be in this film but only in the first act. I think Loki will use the Hulk to battle Thor and the avengers at first in order to distract the avengers from the skrull invasion he is bringing to earth and to make Banner feel as though he can't control the Hulk therefore he won't be able to stop the Skrulls as the Hulk. It's the freaking Avengers, Whedon won't ignore this major storyline of the Avengers lore but it won't be the whole plot of film. Their just isn't enough meat.
That's just my two cents really. You lot are thinking their is gonna be an Avengers 2 but that might not be the case. Marvel need to go all out with the Avengers, as its a huge event and essentially an assemble movement. The threat needs to be huge and bringing in the skrulls is the only logical reason to bring these group of bad-ass mother****ers together.