Barry's decision to travel back in time and save his mother in The Flash Season 2 finale is sure to have dire consequences for all the CW shows. But before we get to that impending four-show crossover, there are some immediate consequences that Barry needs to think about, like the fact that the Reverse Flash has now not been defeated and is now on the run (literally).
In the last moments of the finale, Barry managed to overcome the Reverse Flash and protect his mother. The last we saw of Eobard Thawne, he was unconscious on the floor of Barry's living room, but it's a safe bet to say he won't stay there for long.
This sets up a few options for The Flash Season 3. Barry might manage to apprehend the unconscious Reverse Flash, but by resetting the future he's erased everything that happened in Season 1, which means that Star Labs no longer has that handy metahuman jail in its basement. So it seems more likely that Reverse Flash will escape Barry's clutches, and that has very interesting implications.
The Flashpoint Paradox
It's possible that Season 3 will be a partial adaptation of the comic Flashpoint, a huge event which changed the future of DC Comics, leading right into the New 52 reboot. Reverse Flash was a big part of this storyline.
In the Flashpoint comic, Barry wakes up to find a very different world to the one he remembers. Aquaman and Wonder Woman are leading their two races to war with each other, Batman is Thomas Wayne, and his mother is still alive. Oh, and he has no powers. Barry comes to suspect Reverse Flash of changing the timeline, but he eventually discovers that it was his own choice to save his mother that caused the Flashpoint.
Reverse Flash's role in the comic is mainly to act as a false suspect, although eventually Thawne confronts Barry, revealing the truth. Thanks to Barry's timeline alterations (and absorption of the Speed Force), Thawne is now a "living paradox", allowing him to do pretty much whatever he wants without suffering timeline erasure. So he promptly tries to kill Barry.
It could be that we see something like this play out in Season 3, as the Reverse Flash runs back to the future with Barry. He could then lurk around for a while, acting as the same kind of distant threat as in the Flashpoint comic. Ultimately, Barry might be forced to finally kill his old foe, although he could be spared this task as he was in the comic. But there is another option.
Changing The Future — Again
Instead of following Barry back to the altered future, Thawne might stick around in the past. In Season 1, he did this because he lost his speed powers, but as he hasn't killed Barry's mother in this timeline, he should still be able to harness the Speed Force. Yet, there's plenty of reasons for him to stay in the past, and they're all in order to screw up Barry's future.
When Barry saved his mother, Thawne knows enough about time to realize that this is going to have huge implications for the timeline. If he stays in the past, he can essentially shape events as he sees fit, creating a very different world for Barry to return to.
This would be an interesting plot point for Season 3, because it would allow the writers to do pretty much whatever they want with the timeline and avoid the fans predicting it. Right now, we can guess a few things that will be the case in the new timeline (Barry not having his powers, for one), but with Thawne messing all kinds of shit up in the past, the situation is impossible to predict.
Of course, if Barry does lose his powers like Thawne did, he might end up trapped in the past, in an interesting twist on how everything played out in Season 1. The possibilities for the post-Flashpoint Season 3 are endless (and endlessly confusing) but suffice it to say that this might be the most interesting season yet — and Reverse Flash could be why.