HINTS OF SPOILERS:
Here's my problem: They end up making such a big deal of Logan wanting to spare Lara his own life ("Don't be what they made you", etc), but... everything shitty about Logan's life is actually Xavier's fault, not his or the people who made him. Xavier is the one who accidentally killed everyone and put an end to everything they had.
Also... WHY were there no more mutants? We get the doctor guy saying he did it by accident, but... why/how?
THAT SAID... the first act/hour-or-so was god damn, motherfucking BRILLIANT. Can't say enough about how fantastic and enthralling it is. The whole movie is great, but the establishing act is superb.
And I'd put the Lara/Logan vs The Reavers scene from the ranch in Mexico (when we first really see Lara in action) at just a bit below the airport scene in Civil War. It's THAT good.