We're starting to see the "Avengers" deleted scenes turning up, and a pattern is starting to emerge: The "much longer" original cut of the film may also have been a "darker" cut, and what went out seems to have been anything that might've changed the "colorful romp" energy of the final film. Probably the right idea - they weren't going to out-gloom the summer's other big superhero epic, and to be perfectly honest the blatant 9/11 allusions in the "alternate opening" is cheesy in the wrong way and would've left a bad taste in people's mouths. "The Avengers" was when this genre stepped back into the light, and I'm more than fine with that.
That said, this bit re-introducing Captain America probably should've found a way to stay in. I can see how it would hurt the pacing (Act 1 is a touch on the long side as-is) but it's a really good piece that (hopefully) signals the sort of movie we might be getting from Cap 2.