How was Barry still a speedster in the altered timeline? Or Wally one, for that matter? Without Wells/Thawne to cause an accelerator explosion, they couldn't have gained superspeed (unless some other scientist set it off, which was never mentioned throughout the episode). I hate the temporal mechanics of this show.
And who was the Eobard Thawne at the end? Was that a remnant or a parallel-universe Thawne?
I also had to wonder how Barry could "move" people at breakneck speed without, you know, breaking their necks or causing damage. Take Joe, for example. Barry gave him a shower, brushed his teeth, and dressed him up in a matter of seconds. Water doesn't flow as fast as a speedster moves; it would've taken at least 15 seconds to get Joe in and out. And if Barry brushed Joe's teeth rapid-fire, the good detective would've lost all his teeth.