I just thumbed through this thread...I'm guessing that it is a bit clearer now how IM3 sets up Phase II (Ultron). I find it interesting that we've been told that the real setup for Avengers II is in Cap II. I'm betting that will be where Fury gets kicked out of SHIELD.
While I enjoyed this flick, I had the same problem most of you did, but have explained away most of it to allow me to be satisfied with the movie. Denial for pleasure sake. The fragile armor makes sense if you remember that all of those suits were prototypes that he pumped out in rapid succession to test things out. They may not have been intended to be used in a real fight, but merely been made for him to test out ideas. Why make them with expensive durable materials if you're just testing out stealth mode? Also, having the armor pieces travel 850 miles in a couple minutes roughly matches the maximum rocket speed we've achieved - 25,000 MPH (850 miles in ~ 2 minutes). Having him match that speed with armor bits is about as unrealistic as the rest of his tech, such as the ability to absorb impacts that should turn his brain to mush.
Btw: I'm betting the next time we see Stark will not be Avengers II. I'm betting he makes an appearance in SHIELD - and would not be surprised to see him appear in the post credits scene in Cap II. I think they'll give us snippets of each of the movie characters on the TV show before Avengers II hits.