I always heard the Bryan Singer's plan for the movies was this:
X1: Mutant vs. Mutant
X2: Mutant vs. Human
X3: Mutant vs Evolution (or Humans and Mutants Vs. Evolution)
Dark Phoenix might quallify as 'evolution', but you'd have to mangle so much of the DP arc (Jean has already 'died' saving the team, but it's hard to say the Phoenix force was in the floodwaters, not a star like in the comic)
other ideas for what could constitute 'evolution'-
Apocalypse (my personal choice)
Sentinals (since they always turn on their creator; but Matrix fans will claim Singer stole the name)
i have more, but most would call for MAJOR plot tweeking
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"Yes, it's the Apocalypse alright. I always thought I'd have a hand in it"
Professor Farnsworth