So, my thoughts:
1. Loved the finale, although Barry's agonizing over whether to go back dragged on a bit. Eddie's death was solid, and made sense, because the character had basically outlived his usefulness.
2. Re: the timeline differences. Meta humans could develop through any number of other ways. Like, in their comic book counterparts with freak accidents, mystical objects, and alien tech. The particle accelerator doesn't necessarily have to exist for any of those kinds of things to happen. That said, time travel (which plays a big part in the Flash comics) is...complicated and never really is dealt with effectively. Doesn't matter much, though. I think next season will be fun.
3. I suspect that the appearance of Jay's helmet could herald the "Flash of Two Worlds" storyline, which introduced the multiverse. The show runners have said they'll be using the multiverse this year, which I think opens up a ton of possibilities for where characters can go. And it's entirely possible that Barry will have a "Quantum Leap" style season (or part of season) as he fixes something then tries to get "home" to "his" timeline, similar to what Wells did.