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The movies are self-consistent. It was another era where continuity between sequels didn't matter that much. The span 'X1-Origins' is consistent. "First Class" was supposed to be a soft reboot.
It's always mattered to fans, just not to the writers unfortunately.
Well, they tried to do it until "First Class" (2011). "First Class" was designed and written to be a soft reboot. DOFP was an afterthought.
As for "Quicksilver" and "Emma" in Origins:Wolverine lets just write them off as similar but not the same characters, it's not explicitly stated is it?
What that DP scene does do anyhow is remove the need to include Origins:Wolverine in the OT timeline and that works fine for me, and personally I wouldn't mind doing the same with The Wolverine but like I say there's arguments in favour of it being a follow on from The Last Stand.
"The Wolverine" is firmly placed in Timeline Two (the one following "First Class"), where an alternate version of "The Last Stand" did happen.
How so?
Good question.
At the end of the Timeline One "Last Stand" (the original one), the X-Men were fully active and there was a sense of hope for Xavier's dream. It was a definitive happy ending.
"The Wolverine" is on the same "destructive" path of DOFP (Timeline Two). The X-Men have disbanded. Wolverine is retired. Bad things are happening in the world. And then, in the mid-credits scene, we see the entire set-up of DOFP.
Plus, Xavier has his body again - not the P. Xavier's body he had at the end of Timeline One "Last Stand" - so maybe in the slightly altered version of "The Last Stand" which occurred in Timeline Two, Xavier's body has not been "destroyed". Wolverine is just surprised to see him alive.
Logan is obviously dealing with the death of Jean in The Last Stand and is surprised to see Charles after the events of that film, (but considering the chess scene at the end hinted that Charles was in Eric's head it might not have even been an actual physical Charles?)
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If you really want to tie it all together and attribute it to someone time travelling you could call Deadpool 1+2 the original timeline, then DP creates the events of Origins: Wolverine which leads to the Original Trilogy and both Wolverine sequels, then he corrects that timeline to some extent by shooting Origins Wade but the "Emma" we see in that film time travels rather than Shaw and that creates the reboot timeline.
I think Deadpool inhabits an alternate universe.
Emma Frost in "First Class" was just a mutant living her own time. Shaw knew the future, had an agenda and also altered Magneto's life in 1944. Everything points at him being more than what he seems. He's the catalyst.
I still think you're approaching it more from an angle of trying to make it fit with an idea rather than trying to find an idea that fits through logical elimination and that puts it in the realm of fan-fiction rather from my perspective.