The Q
Hoop’s Villain, Reality’s Hero
Like we saw with the Trajectory episode, the velocity serum makes you faster but it also brings out the evil in you as well (as well as bunch of it will turn your speed lightening blue). It brings out another personality if you will, sort of like what happened with Spiderman's Green Goblin. Recall the scene where she was having a conversation with herself in the lab before she took the serum.
Anyway, he would turn good, simply by getting off the serum as that effect would wear off, presumably. Again, this also explains his fear of the velocity serums and why he doesn't want Barry to take them. Evidently, over time, this is why he lost his speed as well but he has given a couple of reasons for that. First Zoom took it and then it was due to Velocity 6 I think. Actually, now that I think of it, if this theory is correct, both of those reasons could hold true.
To your 2nd point, he does know not to keep taking it... again, that is why he doesn't want Barry to take it. Although, he does take it a couple of times on E1 (to save Cisco and while Barry is on E2) without showing much of a mental struggle. Here, keep in mind though, Jay is(was) dying as well. The idea would be that Jay actually quit using the serum (or maybe just ran out) and became Jay again. He would still be dying and perhaps when he first did this, he still had most of his original speed, so he could travel back in time as a attempt to stop himself. It would just mean that over time, off the serum, it slowly went away.
In a nutshell the time line would be:
1. Well's accelerator blows - Turns Jay into The Flash
2. Jay acts as The Flash for sometime but desires to be faster, then develops the velocity serum
3. Over time, this serum turns him into Zoom
4. Zoom does lots of bad things in E2
5. Zoom runs out of serum or something happens where Jay finds away to escape the grasp of the velocity serum and stops taking it.
6. Jay, still having much of his original speed force travels back in time to what I have as (4) here as an attempt to stop himself(Zoom) from something bad he did. Much like Eobard in S1 though, he gets stuck as his powers start to fade.
One thing that has never really been clear is when specifically did Jay lose his powers. Originally, they said it was when he was battling Zoom on the rooftop and Zoom had him almost defeated but he was sucked through the portal to Earth 1. That doesn't really make sense with the whole velocity serum thing which he now said was how he lost his powers. However, if that is why he lost his powers, and they were already gone when he was sucked in the portal, why would he be fighting Zoom without powers?
I think a Fight Club like theory would have been fun too but I don't see how that works out with Zoom holding a dead Jay. TLDR
Holy moly
Great job. It makes sense.
I'd like to think he could recognize his own uncovered face though. Lol. But again, Superman hides behind glasses....oh well.
Also, copying thawnes story would be a bit weak.
But dude this is about as good of a theory as I've heard so far.
I think the man in the mask is the key to unlocking it all.
Maybe its thawne? Maybe he has time travel ability ans that's why zoom kept him alive. Who knkws.