I am not really going off facts, and also have not ever read any comics, it was before that luxury was even existent to me so yeah.
I was wondering, what if Professor Zoom/Eobard Thawne has created infinite timelines in efforts to destroy the flash? For example, right now on the Flash (CW) he has traveled back in time to kill Barry but kills Norah instead, then he kills the actual Dr. Wells and impersonates him, the creation of particle accelerator is then a part of his supposed plan to get back into his own timeline, but then there is a moment in one of the episodes where he vows (verbally) to kill Barry.
Time Travelling is an interesting factor when its come to these types of situation and this is where I want to insert this theory in. I mean I could write an entire freaking story based on this because its just that exciting!
Professor Zoom / Eobard Thawne travels back in time but his plans do not succeed, instead he allows Barry to live so that he can face him again, this creates the events that led him to travel back in time, repeat because he cannot destroy Flash as a grown adult. Now since he has changed so much already, like taking over Dr. Wells, he has created a separate time line. Whatever he does now, unless they happen exactly like how they were when he traveled back in time, he can't go back, because the "future" for this time line is different than it was where he came from.
Considering the fact that Thawne can travel in time regardless, he gets so mad that he pushes himself beyond his own limits, allowing him to not require physical surface under his feet to actually move. He flies around the Earth so much that within a blink he is in a different time line, where he does exist and is Professor Zoom. Surprised at his new ability, he then reveals his new powers to that time line's Zoom and since they are both from different time lines, they can co-exist. He then creates an army of himself from different time lines to visit each and every single one of them to kill Flash's parents before they even meet.
Zoom's Partial Plan to Kill The Flash Before Existence
That's what was on my mind about Zoom and a lot more because that's just how he plans to defeat the Flash but I think we have all been under estimating the Flash a little too much so I have a theory about equating his powers with Zoom's too. Let me know what you guys think, and then I will write more. :)