I think the show runners have got to be smarter than making Wells into Prof. Zoom.
I honestly think he plays such an important part of the team dynamic at STAR that I can't imagine him completely out of the picture.
They've also taken a character named after Barry's rival (Thawne) and dating the girl he loves (Iris) and made him into a likable, almost hilariously oblivious character that seems to be completely disarming.
I'm not really sure what's going to happen, since it seems to obvious that either Eddie or Wells is Reverse-Flash at this point. But I also hope the series doesn't go deus ex machina with the villain and just pull him out of nowhere.
Also, quick theory: What if Wells is Barry, from the future? Really long stretch I know, but what if Barry grows up to be a brilliant scientist (his mother never dies, so he doesn't grow close to Joe and doesn't go into police work) who finds a way to tap into the Speed Force. He does so, and creates Professor Zoom, who somehow causes the crisis. Barry/Wells decides the only way to stop Zoom is to go back in time (using Zoom's ability to time travel somehow) and turn young Barry into The Flash.
Wells shares enough physical characteristics with Barry that he could be him, just 20-30 years older.
Why does Wells see young Flash (Grant) in the newspaper, in the future? Simple. He goes back in time, makes his younger self into the Flash, and at some point Barry goes forward in time and stops it from happening. Now, that would be a twist.