If this show ever began to get stale, or they wanted to shake things up, they could easily change the timeline, restore the original or have some Flashpoint paradox. It would be like a reboot of sorts, but with people occupying slightly different roles. That could explain why Caitlin could be more villainous, and it could even have Dr Wells as a genuine ally. If only Barry remembers what his "original" timeline was like, he would find it very unsettling having to work alongside someone like Wells who would be a genuine good guy, knowing that he thought of him as an enemy, while squaring off against Caitlin, remembering that she was a trusted friend.
In other shows like Eureka, they have proceeded with an alternate, altered time line for the remainder of the series as a means of a reboot of sorts, or at least to change a few things about the series.
I wouldn't mind seeing Wells as a sincere good guy helping Barry, while facing off against the real Eobard Thawne. Thawne could become an actual enemy to Wells as well as Barry, because Harrison would know that Thawne was responsible for killing his wife and stealing his life from him, and using his good name for evil purposes. All that STAR labs should have been and what Wells would have intended it to be would have been corrupted by Thawne. That is a big reason enough for Wells, if he were somehow to come back, to also see Thawne as his arch enemy.