The big question of course is: If Wells is Professor Zoom, who the hell is the other superfast guy, in the yellow suit, who the beat the crap out of him?
Was this a future or past version of Wells or could it be that it was plain Zoom, with whom Wells is working together. And why does Wells need the Tachyon-generator for? To become Professor Zoom or create the other Reverse-Flash instead, which would also include time-travel shenigans.
Time travel is the cause of many headaches. I suspect that Wells/RF traveled a bit into the future so that he could be there as RF and beat the tar out of himself.
Also as proof of Wells being RF, despite such a pounding Wells received and yes they have him first aid, did he really look all that injured at the end when he revealed the RF costume in his secret room?
Also he spoke in the modulated voice of the Reverse Flash so that pretty much clinches it, unless they pull a hat trick as it were and show there are TWO Reverse Flashes...