Almost done with the IA story and i can say this.
No other story has the outcomes the IA has. Your early on choices will affect the outcome in major ways unlike many of the other stories.
I have read about this and I actually think this is a bad thing. Because the endings are so different that the writers will have a hard job trying to tie them all together in an expansion, assuming there is a single questline for all Agents. Difficult things are generally done last