The episode of JLU with the Flash Museum shows exactly why Wally should be the Flash. He isn't your a-typical hero who is out for pure justice, black and white, blah blah blah. He sees his "villains" as people in need too and does his best to empathize and help them. One of the reasons the Rogues are the most interesting group of villains is because they know how ridiculous dressing up in a costume is, and they know exactly why Wally is stopping them, and actually understand his reasoning, don't take it personally, and are making personal choices. And now, with Barry's black and white attitude, they are back to being thug, joker-knock offs.
I just do not understand this at all. Who knows the Rogues and Wally dynamic better than Johns?
And yes, it is possible that he's going somewhere great with this. The fact that our concerns are being addressed in the freaking book is astounding. I am interested to see where it goes and hopeful he doesn't alienate the last 20 years of flash fans.