I think we will find that CA:TWS will probably take place in the same timeline as IM3. Steve is really the only one suited for helping Tony.
Also from what I understand, the President in this film is upset that the US Military was unprepared for New York. He probably doesn't want SHIELD's involvement, who operate as more of an international autonomous organization, with Fury ignoring the international council of leaders who he is supposed to be under the command of. That would eliminate Fury, Hawkeye and BW. There was a rumor at one time that Val Kilmer was to play an unnamed SHIElD agent, taking over for Coulson that would be assigned to Tony, but that part of the script was rejected.
Banner only unleashed the Hulk, because he realized that it was the only way to stop what was going on. At the beginning of TIH, it has been several months/years since the Hulk was unleashed, and between TIH and Avengers, BW mentioned it has been more than a year since he's had an "incident". Banner will be reluctant to unleash the Hulk again.
With Thor it's pretty obvious. From the TDW trailer, we know the Bifrost will be repaired, but we don't know what the timing will be.