^ It all depends...
If they want to have the cause of the Age of Apocalypse be what Wolverine changes in the past, then him "waking up" back in the present, but it being a different present, controlled by Apacoalypse, just makes sense. It leaves us on a cliffhanger for the next movie.
But if instead they want to explore the whole Xavier dying in the past, murdered accidentally by either his son or someone else (maybe First Class Magneto - but there would need to be a catalyst caused by someone in the future coming back)), which causes Magneto to run the school and the Age of Apocalypse to happen, then a different ending for DOFP makes sense.
Actually, these two could be combined. Imagine in DOFP that Wolverine coming back causes Mags to accidentally kil Xavier. Wolvie ends up being sent back to the present, but it's a changed present (Age of Apocalypse) caused by the death of First Class Xavier...
Hmm... I like this!