Lol. Very nicely summarized.
Since Logan is the center of the universe and has to be related to everyone and everything, the creators could possibly further justify why Xavier put Logan incharge(excluding the reason Scott couldnt function without Jean) by showing a flashback episode where Xavier fought alongside Logan in a war. It does appears like Xavier has known Logan before he formed the X-men, especially since he only has telepathic sessions with him, freezes Scott for intruding on the session and prepared to have Jean killed. And let's not forget having the time to ego-feed Logan from the future
Such a revelation is possible. Xavier was in the army before he founded the X-Men and it could be possible he ran into Logan during that time. He got to run into Ororo as a child thief, after all.
I saw Future Xavier basically choosing a horse he figured could perform better than Cyclops and had proven himself by reforming the X-Men before they were able to access him from the future via his comatose body. Xavier knew Cyclops didn't have those kind of chops even in the best of times, and certainly didn't at his lowest.
At best, it was akin to the 90's when Bruce Wayne personally picked Jean-Paul Valley, and not Dick Grayson, to become the next Batman when he was crippled. The logic was Bruce was too close to Grayson and knew him too well; he felt Grayson was probably too emotional or didn't have the moxie to pull it off properly. He knew Valley more objectively and felt he had the drive. As it turned out, Valley was almost a sociopath, and had to be taken down. Of course now, with Wayne dead, Grayson is now Batman. One could argue in the same way that is why Xavier has chosen Logan and not Cyclops as his prodigal son. Whether that is accurate or whatnot to X-ideals is the debate.
From what I've read of the character, he could potentially pull off the leader position, he just never had the inclination to, because Cyclops was always the leader and, by his mini, was in constant conflict with his animal nature. The initial episodes weren't bad in his taking charge, though they never did establish exactly what Logan did to change the future as leader of the X-Men...
Yeah, but didn't Wolverine and Mystique have a relationship back in the comics too? I think they just moved it from the '20s to have it happen around his Weapon X period.
In the comics, when Cyclops wasn't the leader, Storm usually assumed that role. Claremont spent a great deal of time in the 80's all but implying that she was the ideal leader because it wasn't "handed" to her and she could even pull it off without her powers. Through sheer strength of personality she could get Wolverine to back down, where he and Scott usually almost came to blows at various points. Logan often got along very well with Storm.
(It could be worth noting that the first time one of them DID take a swing at the other in the comics, it was Cyclops only a few issues after Giant-Size X-Men. Logan was chewing him out for not shooting down a fleeing Eric the Red, along with a brainwashed Lorna and Alex, and Cyclops backhanded Wolverine across the face with a closed fist. Granted, that was back in the 70's when Logan not only wasn't popular, but fans were almost urging the writers to kill him off. Until Bryne got aboard he was usually dismissed as a "psycho".)
In fact, one of the few periods in the comics when Wolverine DID lead the team was when Storm all but ordered him to over his own objections. Later on in the late 90's, Rogue led the team after outwitting Logan in some training exercise. That was around Claremont's first "returns" to UXM since leaving in 1991.
Wolverine had some thing with Mystique in the past, but he's Wolverine...he has some THING with EVERYONE in the past. Xavier, Mystique, Captain America, Agents of Atlas, etc. That's sort of why it almost becomes a parody of itself. Usually in the comics and even prior cartoons, Nightcrawler was the one with ties to Mystique, and later Rogue in the 90's. EVOLUTION handled that astonishingly well. It only gets frustrating when writers claim how terrific a character Logan is, yet they then turn around and have Logan outright leech story plot points that used to belong to other characters. If he's so great, he doesn't need that, and I don't think he does, honestly. Han Solo is awesome without having to usurp a role Luke or Leia have.
Pretty soon we'll find out that Logan was, in fact, Adam, in the Garden of Eden. God gave him amnesia and it writes itself. Call it WOLVERINE GENESIS and it'd sell 85,000 copies, easy.
