I can only make this comparison, you know how Kang is from the far future and has conquered numerous timelines but every now and then still goes back in time and finds himself against the Avengers? I'd assume it's like that on a lower level.
I highly doubt Barry has lived that long to still be Thawne's enemy. So I have to assume for w/e reason Thawne keeps going to the past when Barry is older to face him. Maybe he time traveled by accident (or to meet the first speedster) and got hyped to meet the Flash then they had a falling out. Thawne may have the personality and thought process that because he's a speedster he's better than everyone else and can do w/e he wants. Maybe a GOD complex. Thinks Barry should be the same way, they fight (you know the typical plot for something like that), and now Thawne sees him as an archenemy so he keeps going back in time finding ways to beat/kill Barry until he comes up with the plan to kill him when he was a kid but future Barry stops that too.
But I could be wrong about all that since I too don't read Flash comics. I think it'd be even more wild if speed powers gives you immortality in some way though
Nah that's just reaching.
He needs to keep up the facade of being Wells. He has to act like Wells. So if he has friends and family he can't use his wife's death as an excuse not to talk to them for 15 years. He needs Wells' memories to properly pretend to be Wells. Given he even had that device on him I'd assume he must've done it before and knows what's necessary to pretend to be another person.
If all he needs is the AI then he doesn't need to be Wells AT ALL. He could just create a fake id, make a fortune, and build the accelerator himself without having to change his entire body and face.