Wells is definitely Professor Zoom. The proof is in the costume itself: Professor Zoom originally only had speed when he wore his uniform. Today, we saw Wells apparently powering up his suit with that Tachyon thingy (demonstrating that this version of the character doesn't possess powers himself).
But wait! Professor Zoom and Harrison were in the same room at the same time! In fact, Wells caught a beating from that yellow suited fiend! How can that be?! Easy.
Tachyons are theoretical particles that move faster than light. They've been a staple of time travel in fiction for decades. Zoom was Wells from a set point
in the future, using the suit that had already been powered up by the Tachyon device: He traveled backwards in time in order to steal the device for his
younger self, (roughing him up in the process to help with his cover) thus creating a closed loop that would ensure his own success.
Q: What was the crisis that caused Barry to disappear? A: Barry went back in time to prevent the murder of his mother. If Barry succeeded, then Wells/Zoom would cease to exist, because why would Barry become a forensic Scientist obsessed with solving crimes (and putting himself in the path of that lightning bolt) if he had a happier childhood? No gloomy scientist = No Flash = No Professor Zoom, so 'Wells' went back in time to prevent Barry from Erasing everything. He succeeded, (possibly killing the future Flash in the process)but at the price of becoming stranded in the past.
Q: Why was Wells trapped? A: Wells doesn't have any powers of his own. His suit is powered by Tachyon energy. After traveling to the past to kill Mrs. Allen, and fighting the Flash, he ran out of energy and was reduced to waiting a couple decades for the era to produce tachyon technology that he could acquire.
Now that his future self has acquired it for him, his suit is powering up right now, which explains why we won't see the Reverse flash again for a while. Which means we should expect to see an episode told exclusively from Harrison's perspective. (The suit finishes powering up, he runs into the past, he threatens Iris to scare Joe, beats up Barry for old time's sake, then steals the Tachyon Machine to give to his younger self, thus setting up the loop.)