There's no excuse for why there was no fire-bird, IMO. Very BAD decision. It didn't even have to be literal fire bird, but the 'psy-fire' Jean was displaying in X2. Just some sort of homage to the comics. Why they left this out, is beyond anyone's guess.
I do actually kinda like the explanation with the water, and how it came into effect with the final battle scene, and I like how Jean 'glowed' when she came out of the lake for two seconds, but still...the 'fire' effect should've been there too (and normal burning objects behind Jean doesn't count).
My major problem with the whole thing is that it appeared in X2, for all to see. Why not build on what was established? It sort of kills the final scene in X2, IMO.