Yes, I did mean Earth-3 in the above title. No, I haven't forgotten that Jay Garrick is from Earth-2 and not Earth-3, but what if Zoom is from Earth-3? Suppose that on Earth-3, Zoom has already attempted to kill the Flash (whoever this world's version of him is), and has either succeeded or been forced to flee, causing him to move on to Earth-2? That could certainly account for why he only appeared on Earth-2 two years ago. But I know what question you're probably asking yourself: "Why Earth-3?" It's simple. What if the scene in "Flash of Two Worlds" where a tour guide is showing a school group around the facility is actually happening on Earth-3? Before you say that there's no proof of this, let me say that there actually is.
We know the above shot is not from Earth-1 because STAR Labs is in mint condition here while on Earth-1, (our world), it still bears the marks of structural damage caused by the particle accelerator explosion. It is implied that in Jay's world, (Earth-2), STAR Labs went defunct following the accelerator explosion, so it can't be Earth-2's STAR Labs either. This logically leaves the conclusion that what we are seeing here is actually Earth-3. Further evidence exists in the fact that when the tour guide introduces the school group to this Earth's Harrison Wells, he appears to be much younger than he did on Earth-1.
Granted, this could be imagination or lighting or any of a million other factors, but Wells certainly appears to be younger in this season than he was last season. Now that brings up the question "How could he be younger?" Well, to answer that, we have to go to this...
In the original comics, Zoom is technically not a speedster. His ability is to slow down time so he appears to be running at super speed. A possible side effect of this ability is likely that he doesn't appear to age as quickly. Now if my theory is correct and Harrison Wells IS younger this season, could it be because he's Zoom? Obviously, it would be pretty lazy writing to have the same character be a different villain every season, and I'm pretty sure the writers of this show are aware of that and have planned accordingly. That being said, even if Earth-3's Wells is not Zoom, he could still have felt the effects of Zoom's games with the timeline, causing him to appear to age more slowly. But how does Wells' appearance on Earth-1 fit into all of this?
I believe that Earth-3's Wells is the man who rescued Barry from King Shark. But then how did he find the speed cannon, and how did he know where it would take him? My guess is that even if he is not Zoom, he somehow knows enough about Zoom to know that he would target Barry. Maybe, on Earth-3, Wells is actually the Flash, which is a possibility, especially considering how the tour guide introduces him to the school group. She specifically refers to him as "the savior of Central City". Now obviously, that doesn't necessarily prove that Wells is the Flash because she could be speaking about him saving the city through technological progress, but if Wells IS Earth-3's Flash, it would certainly explain how he has so much knowledge about Barry and Zoom. It would also explain why Jay has only had to deal with Zoom for two years. If Wells is Earth-3's Flash, suppose that Zoom was wreaking havoc on Earth-3, but Wells' scientific genius was too much to handle and Zoom moved on to Earth-2? Knowing that Zoom is now commuting between Earth-1 and Earth-2, suppose that Earth-3's Flash-Wells decided to follow him in an effort to find his two fellow Flashes (Barry and Jay) in the hopes that the three of them can defeat Zoom together?