This film definitely didn't ignore X3 and I really liked that when I was watching The Wolverine!
The upcoming films will not make Origins/X3 any better if they are just gonna ignore them or continue retconning things that are really noticable. Good thing, The Wolverine didn't hurt the continuity.
"This is our chance to make a difference" - Sue Storm - The Invisible Woman
"He's stronger than any of us but he's not stronger than all of us" - Reed Richards - Mr. Fantastic
"We could these powers to help people" - Johnny Storm - The Human Torch
"You can't fix this, nobody can" - Ben Grimm - The Thing