Originally Posted by Mrs Vimes
Alternate future was what I thought of as well. Apart from it being the easiest option, to me it seemed that placing the Sentinel future post-X3 kinda deals a crappy hand to the X1-X3 characters. Once you change something in the past, either their whole timeline ceases to exist, or the action creates an alternate (reboot?) timeline with the alternate versions of the X1-X3 characters. So every time I'd watch X1 or X2, it would be kinda depressing to think that all those characters have nothing much to look forward to, and that Professor X's dream of coexistence eventually comes to nothing, in this timeline.
Judging by the most recent comments though, it seems that DoFP is set post-X3 after all.
I say wipe the slate clean. The X-Men movies are about Wolverine. It would be a good way to complete his arc, should he go back in time and prevent the mutants he loves from dying. That would be worth it, and an acceptable explanation to do away with the events of X1-X3. Of course Magneto would see the errors of his ways at some point and would lose interest in Rogue, hence Rogue never ends up joining the team because the Brotherhood never bother to track her down. So Rogue doesn't become an X-Men either, although you can write her back in at some point if you choose. Maybe she is recruited another way.
I think you need two films to wrap it all up, so make a third movie picking up in the 80's with Cyke, Jean, Beast, Storm, etc. Have Sinister as the villain. Then you can take a break from ensemble movies for a while. Wait for the new cast to get older. Post X-3 trilogy in 10 years time.