Aren't we all used to the idea of other heroes mysteriously disappearing while we read titles devoted to just one character? What's the big deal?
I don't think there is one. At the end of the day, it's like a lot of other things: Marvel has created this universe across several films, so how they handle that will be part of the discussion.
Apparently with this film they wanted to make sure it focused on IM/Tony Stark without any crossover material.
I think it was probably the right choice. We'll see how it plays out in the other phase 2 films, but they want the solo films to work as solo films, and they want the crossovers to feel special. Not just another day at the office.