Crazy theory in regard to Wells:
An Earth 2 Wells would be sort of boring. Especially if he is only just Wells. Is it possible that Thawne, anticipating the actions of Eddie (arguably even driving him to it), simply switched Eddie of another Earth with Earth 1 Eddie? He did kidnap Eddie shortly before his defeat (and his motivation in doing so was never really elaborated on). It would explain why the timeline is still intact. Maybe it was Earth 2 Eddie who killed himself and Thawne "disappearing" was actually Thawne teleporting to Earth 2, to assume the identity of their Wells, in furtherance of his plot. In essence, it was a gambit to take him off of the Flash's radar and allow him to accomplish his true goal (which wasn't to get back home, but rather get to Earth 2, undetected by the Flash, for some reason).
This theory could raise two possibilities, IMO:
1) Wells is Zoom (which I don't buy)
2) Zoom is Earth 2 Barry. Perhaps that was Thawne's ultimate end game all along...to somehow corrupt Barry. First he tried to do so by taking his parents. When that failed and Barry remained relatively well-adjusted, he became Barry's mentor. When he finally learned it was a lost cause on Earth 1 and that Barry could not be corrupted, he modified his plan and went to Earth 2 where he "created" Zoom.
Just a thought, anyway.