Well the casual explanation behind phoenix actually worked quite well, how else would they have described it, Unlike the comics she didn't fly a space shuttle and get posioned by radioactive waves and get an offer from an outside force which replicated her body and took some of her essence, They had to make JEAN the phoenix not some outside cosmic force this is the only reason for the flash back, it told the people who didn't know the real story that jean had always been powerful and the only reason she wasn't as powerful in the first two movies was because of the mental barriers Xavier put up in her mind, this forced her unconscious to develop an alternate persona because that persona- linked directly to the power she was blocked from- was a reflection of the power itself, hence Jean is the phoenix and instead of a replicated body made by the cosmic phoenix with a portion of jean's life force in it they used another side of jean a kind of metaphor for the replicated body in the comic. It could be said that the use of cerebro in the first film and the electro magnetic pulse that rogue powered up had started corrupting the blocks in her mind to allow her to start reaching her full potential and she did