Yeah, the rights thing is stupid - that's the reason why Quicksilver and Scarlet Witch weren't in the movie, and why the Chitauri were the villains rather than the Skrulls. This just doesn't work for Marvel movies - all characters are supposed to occupy the same universe and be able to appear in anything.
I think Quicksilver and Scarlet Witch weren't in the movie because it would be pretty weak to have them in there without anything Magneto being done with the universe yet. You can't really delve into them too far because of that.
And they clearly kept the Skrulls away from the movie for the Fantastic Four, which is perfectly fine. That means they want to use them later. Nothing wrong with that. The Chitauri were fine for the blanket random enemies they were supposed to be.
And just because they have chosen not to involve certain characters doesn't hurt the movies at all. They'll get the rights to the Fantastic Four eventually, and they'll get to play ball with them.
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Down with Zhang. Let there be Biscuit!