First of all, I love this movie and welcomed Bryan Singer's return, as I always loved the first 2 films. I understand that he doesn't particularly care for the films he didn't direct, and that his goal here was to "fix" what he didn't like, but he flat out ignored several things creating more continuity problems before the timeline change took place. First off, The Wolverine ended with Logan losing his metal claws, something that could have been interesting to explore rather than bringing them back with no explanation at all. The biggest gripe is Xavier though. He obviously is destroyed by Phoenix in X3, although the post credits scene reveals he came back in another man's body. In the Wolverine, he reappears to Logan as himself, and the tease("you're not the only one with gifts") suggests it will be explained how he is back in his old body. I know there's a book that says something about a twin, but we shouldn't have to rely on a novelization to give us continuity for the films. Other small things, such as pretty much ignoring everything from Origins, just all seem like a petty way of dissing the movies that Singer wasn't involved in.
The problem with the two things you brought up is that it's difficult to explain them in a narrative which involves a time jump like this without it coming across as feeling as though you're talking directly to the audience. The time to explain Xavier's situation was right after Xavier's line at the end of that Wolverine mid-credit scene. ~10 years later all the characters already know what happened so you can either risk ruining the pacing by putting in an unnecessary flashback, you can have characters bring up something that is old hat to them and thus risks us thinking they're not talking to themselves but directly to us, or you can trust audiences to come to their own conclusion of what might have happened.
Singer originally wanted to insert his own explanation, not about the twin which was the original idea behind that Last Stand mid-credit scene, but about a mutant reforming this new body to look like Xavier's old body. He ended up scrapping that, probably because he realized it couldn't be done without creating more of an issue than the one it solved.
Same thing with Wolverine's claws. Frankly, it's so easy for him to get his adamantium claws back and so important that he did so given that they were up against sentinels and he was useless without them that it would feel contrived if he didn't have them here. I agree that it would have been interesting to see him struggle without them and then have to go get them back to overcome a problem but the time to do that would have been in a movie set directly after that Wolverine mid-credit scene and while it would have been nice to see that the technical difficulty involved in pulling off a movie that utilized the original cast for the entire length of a film prevented that from being possible. Thus, instead we have a time jump and information that the audience is trusted to figure out on their own. No, we don't know exactly what happened, but we do know that he got them back and we can put together a couple of likely possibilities as to how that might have happened. The most popular one is that Magneto helped him out, which is something that Singer also said in an interview.
Time jump or not, btw, all narratives balance trusting audiences to piece together likely information with flow, pacing, and believably of information coming out onscreen. Take the first X-men movie as an example. How did Rogue get to the train station? We don't know because they cut from her being convinced to run away to her being there. She didn't have money so she couldn't pay for a taxi on her own but it's not impossible to think that she might have gone into someone's room and taken money out of someone sock draw after seeing that exchange with the tip jar earlier in the film or that she hitch hiked there so it doesn't need to be explicit; having Wolverine ask Rogue how she got there after the fact or showing it happen would have just slowed down the movie.
Similarly, people often ask how Sabretooth found Rogue in Canada and there they put together clues that allow audiences to figure it out and trusted people to be able to do that. You have the map in her room where she marked her intended path, a shapeshifter who can pretend to be the police officer to gain access to her room, and a tracker who was in Canada looking for her by himself, suggesting that he might have been sent along her planned path to sniff her out. It means you have to pay attention and use a degree of critical thinking, again, not to determine the definitive answer but likely one. That, though, is simply how fiction and life, actually, works. If a gap creates contradictory information that lacks any reasonable solution (not like that nonsense that Knowby_Warrior peddles) then that's a problem. Otherwise, it's just standard fare.
"Knowby's theory is technically fan fiction, but it works, given what we know about time travel in the X-Men Universe. The fact of the matter is that the divergences started happening with First Class (not Days of Future Past). That movie introduced a bunch of continuity errors. But since DoFP followed up on FC and showed that a bunch of the events from the original trilogy still happened, Knowby "created" a time traveler to account for all the minor changes.
And this works because, as we see in DoFP and Apocalypse, time keeps flowing in the same general direction. You can tweak things here and there, but some events are bound to happen.
As for Logan, we'll have to wait and see how it fits in. There might be a new timeline called the "Meta Timeline", where you can fit movies like Deadpool and Logan. They're more commentaries on the X-Men franchise as a whole than particular episodes in a long running series."
Ad Hominem has never been a valid argument, and it still isn't.
You can't dismiss someone's well-thought arguments and thoughts just by insulting them to be a 'troll', thereby also revealing your own ignorance as to what 'trolling' really means, where it originated and so on.
In my opinion, someone that doesn't even understand basic concepts like the difference between 'troll vs. trolling', isn't qualified enough to write anything meaningful, much less an analysis on a movie that makes no sense, or a well-written, well-argumented, well thought-out post about multiple such movies' timelines and narrative expressions.
The kind of mind that thinks it's clever or even acceptable to just say "[Name] is a troll.", and thinks it conveys anything meaninful, other than revealing its own ignorance, arrogance and dismissive 'I won't listen to you, I will put my fingers in my ears and sing la la laa very loudly'-attitude, is the kind of mind no one should ever listen to in any circumstances.
No offence, but your kind of 'argumentative style' (insulting someone and declaring victory) is extremely childish and comes off as someone that just doesn't understand his post, and anything you don't understand, you have to attack and insult. Not cool.
I'd rather die in a housefire than listen to you screaming 'fire' and considering its possible reality and run out.