Re: "Mr. Stark, you've become part of a bigger universe."
Well I prefer that they would go towards the second approach, but I can see the disadvantage listed.
I think the problem is that Marvel are in such hurry to make Avengers that they may have made Jon put in the after credits scene without considering the continuity. I would have prefered to have the Nick Fury and Tony Stark scene somewhere in Iron Man 2 or Iron Man 3, not in the first movie.
Also I think Tony Stark scene in TIH didn't really help much either in clearing up the continuity - how long has it been since Stark revealed that he is IM (and meeting with Fury) that he went to visit General Ross?
But oh well, what's done is done - so we'll just have to wait and see.