Yeah, one movie was clearly written for one model (Phoenix was just Jean's powers switched all the way on), while the other was something completely different (Phoenix was only Jean possessed by the space energy). At this point, I don't think there's any point to worry about X-Men continuity anymore; beyond the fact that the series is over and done (aside from New Mutants, which is apparently scrubbing all references to the series, anyways), it's just a mess. Enjoy them for what they were and just leave them at that.