Morrigan = the most awesome character in the DA universe by far.
I hope she comes back as unaltered from DAO as at all possible, because she's quite perfect in DAO.
As for her being a companion in future DA - that would be rather nice, and a major selling point for me personally. As for the potential problem, that a her as a romanceable companion would screw up the Warden+Morrigan romance of DAO with a new protagonist - well just make her romanceable only if the DAO warden was not in romance with her at the end of WH. Problem solved! Or just not make her romanceable at all.
She could easily have left the Warden behind in Eluvian land for whatever reason, or got seperated from him some other way. Easy to fix storywise I'd imagine.
Ofcourse the really great solution would be Warden as possible protagonist - then the problem goes away all together, but sadly the devs do not seem eager to grant us this humble wish