I'm sorry, but time travel is the PERFECT opportunity to rewrite the events of The Last Stand and create a new timeline (like the recent JJ Abrams Star Trek film established it's own timeline) and I REALLY hope Singer takes advantage of that. :P
Logicly It would be strange for Bryan Singer to be directing and rewrite his own films(X-men/x2) He has also talked about connecting films and connecting
dots between films.That's kinda hard to do If A:Future Is just alternate version of characters from earlier films(now this Is possibilty) and B:If time travel does away with all X-Men films besides First Class and past part of DOFP(that would keep the X-Men films In past)
The Wolverine has been said to connect to DOFP.Kind astrange they would do that and a year later wipe the Wolverine out of exsistance.Plus I find It strange fox wouldn't want the opotion of a third wolverine film.
If you go the Star Trek path you still have limitions on you.If first era sequel to DOFP Is still In 1960's It wouldn't make any sense for characters that were young In mid to late 1990's/2000 set trilogy like Rogue,Iceman,COlossus,Kitty,and Angel to show up.Now would It make sense for characters like Cyclops,and Jean to show up as Teenagers when Xavier Is barely In his early 30's
Considering past work It's easy to assume certin things that are likely from Bryan Singer.Add to that his comments.This Is a 2 hour film to have characters from both earlier films and first Class It's very unlikely they will flood the film with new characters as some on boards have speculated.What purpose would characters not In DOFP like Cable or Bishop really serve.
I have had to listen to a lot of whining about First Class not being like comics yet some are advocating the film version of DOFP have little or no resembalance to comic version.
I personally think It's more likely they would use time travel to wipe out events of Last Stand giving them opotion to do something else with original cast members without that film In way rather It be another X-Men sequel,a third wolverine film,or more present day spinoffs.