Originally Posted by Mr. Dent
I think when the guy said it's the wrong question, he means we shouldn't be asking whether he's in the film or not but how big a role/how relavent he will actually be to the plot of the film. Tony might be incapacitated throughout the course of the film...we know Thanos is involved so there you go.
I think you've nailed it.
Conjecture, of course, so I won't spoiler-tag it, but maybe what happens is this:
*End of IM3: Tony test-flies his new Deep Space Suit. For whatever reason.....mysterious signal from space, possible new alien threat, he's going looking for Peter Quill for whatever reason --- anything. Turns out that Thanos is luring him into a trap, and captures him.
*End of GOTG: After all the events of GOTG, in which the gang presumably takes on Thanos unsuccessfully, they learn that he has an earthling captive: Tony Stark. Hell, just to mix it up even further: maybe he's even mind-controlled and enslaved to Thanos' will. Or maybe not --- that's just bonus stuff.
*Avengers 2: Tony Stark *is* out of commission. He spends, say, the first two reels as Thanos' captive, and is rarely if ever seen. That leaves the Avengers and the Guardians to team up and not only take down Thanos, but also the mission becomes much more "personal" (remember that quote....?), because they're trying to save their friend. Third reel features Tony back in action, and the whole gang gets to whale away on bad ol' Thanos.