Yeah it does seem that a lot it comes from ignoring stuff in X3. That's fair enough, I thought it was a crummy movie too. (Even though maybe it does come off a bit snobby from Singer perhaps)
But anyway, it seems to me the only point of ignoring X-Men: The Last Stand is if let's say Singer made an X-Men 4 that ignored 3 and carried on from 2. (X-Men 2.5, whatever you'd call it. I suppose "X-Men 3" could be used, I'll just call it X4 for the purposes of this next bit)
But let's face that won't happen. 'Second Class' I'm fairly sure will happen... so it's 2011 now, let's say that comes out in 2013, and Third Class in, say, 2016. I doubt X4 would come out while those were being made, so then that wouldn't be able to be released till, what, 2018?
Now it's 2018... fifteen years after X2 came out. Are you gonna use the same actors? Anna Paquin would be 36, Hugh Jackman 50, Ian McKellen 79, Shawn Ashmore 39, etc etc
It couldn't exactly take place right after X2, so how do you explain the 15 years. They might as well recast........ which would make me think, why bother with it at all? Just reboot.
So basically my thoughts, are, haha, I hope the movie X-franchise continues, but it sure ain't gonna be tied together all nice and tidy