This is the last film, as far as the X-men goes. Hugh Jackman has confirmed it during various interviews along with the fact that Fox is developing a Wolverine film and a magneto one. He even said that he spoke with one the execs at Fox and he pretty much said that The Last Stand is final chapter of the series.
When Brett Ratner took over as a director from Bryan Singer he also hired new writers since Bryan took the original screenwriters with him when he agreed to do Superman Returns which also stars James Marsden aka Cyclops (which would explain his limited screen time in this film). So, I assume these new writers wanted to go out with a bang and not write a formulaic script where everyone lives happily ever afterwhile also tying up loose ends.
And if you stayed and watched the end credits, there's scene where we see Xavier ressurect himself in a catatonic patient. Earlier in the film he was talking about how someone like him can put his consciousness into a well, a catatonic patient. So, he still lives on just in another's person's body.
The final fight between Wolverine and Jean was heartbreaking. It reminded of the season 2 finale of Buffy where she had to kill Angel in order to save the world.