Having just seen The Man in the Yellow Suit the fact that this episode borrowed elements from Mark Waid's The Return of Barry Allen is unmistakable - the emphasis on Barry's trauma over his Mothers murder is a particuarly telling detail as it is built upon his loss of power earlier on in the Lightning Man episode, which was said to be partly him blocking his own power. So as the Reverse-Flash overwhelms the slower speed-of-sound barry it is replaying Wally West's identical disparity with his clash with Reverse-Flash. Wally comes to realise he is guilty himself of not tapping his true potential, and here in the tv series it seems quite clear to me the producers are using the same paradigm with Barry.
So considering everything that the time travelling Wells has done is revolving around making young Barry as miserable and self-doubting as he can perhaps his motive is simply to intervene with Barry's real history and make sure he is not reaching his true potential. That he will never become the same calibre of hero and force which Wells/Reverse-Flash knowss of in his own future...
Still think that the Zoom flash is more than just Dr Wells alone though, and that somehow he needs barry ro be all that he can be in order to make sure the Flash averts the coming Crisis event!