Yeah. I was expecting a flaming aura around jean, but did we get that? no. we never saw her actually rise out of the water. shame...you can tell this movie was rushed in a poorly manner because of what went on behind the production. I wish Singer didn't leave.
As I suggested in another thread, the best thing to do here is to have "Dark Phoenix" from X3 turn out to be Madelyne Pryor. A clone/reproduction of the real deal, explaining why we didn't see all that we would expect to from Jean as the Phoenix.
Sinister cloned Jean, kept her and Scott captive, and what we saw in X3 was a result of his genetic musings. IMO, it cleans that mess up nicely.