In a way, this whole mess is Flash's fault.
Not only can we pin the birth of the multiverse on Jay and Barry running to save the same construction worker, but by referencing older Golden Age characters a sort of proto-continuity was born. If Flash wasn't the first DC hero to routinely go backwards and forwards in time, then he certainly had the most frequent time traveler miles. Plus there's the whole Flashpoint mess that's leading up to DC's "don't call it a reboot" reboot.
Flash himself is a bit of a conundrum (and I'm talking Silver Age and forward Flashes here, so mainly Barry, Wally, and a bit of Bart). He is, hands down, one of the most powerful characters in the DC universe. His access to the Speed Force, a nebulous source of power and power creep, lets him do a whole host of things from punch with the weight of a white dwarf star to vibrate through solid objects and even into other realities.
And yet he spends his time fighting petty crooks armed with snow parkas and boomerangs. What?
I think Flash is afraid of his power. Of the A- and B-list heroes, only Flash came into his power by accident. The rest were either born that way or chose to become that way. Even C-listers like Captain/The Atom(s) sort of knew what they were getting in to before they ended up with powers. All Barry (and Wally) did was leave a window open in the rain. Barry's previous experience as being a CSI gives him absolutely zero leg up on how his powers work and how best to use him, just some motivation to use them to fight crime.
Barry is scared of what he can do. And the reason for his fear? The Speed Force.
Barry is not the first person (maybe the first human, though) to gain access to the Speed Force (say, .7 SU ago), but in the Drewniverse, he's certainly held onto it the longest by far. Most people when they get hit by that lightning bolt out the blue start running, testing their limits. Except there are none. They just keep going faster and faster, lost in the joy of velocity before eventually fading, subsumed into the Speed Force itself at some point of singularity. Then the force continues on, moving through time and space, until it runs into its next host. Then the process repeats itself. This has gone on since the beginning of time.
The Speed Force is the motive energy that keeps the universe running. That Barry still holds on to it and repeatedly shies away from giving himself over to it means that universe is starting to wind down, to wobble a bit like an out of tune motor. This isn't a dire situation - I doubt that even if Barry was the Flash for a hundred years that it would cause irreparable harm - but it could explain some of the other weirdness that is starting to crop up on Earth. Like a rock thrown into a pond, the Speed Force landing on Earth and stopping has sent ripples out into time and space. Maybe it was those ripples that turned a Kryptonian escape pod towards Kansas? Maybe it's that miniscule wobble they cause that's making a shrouded island to reappear before its time.
We're sticking with Barry Allen here, mainly because I used to watch that horrible Flash TV show with that guy who plays the jerky husband in all those Lifetime movies in the title role. I liked Wally in Justice League (the end of the Cadmus arc with Flash vs Braniac/Luthor still makes me fist-pump), but I think that minimal attachment portrayal works better in an ensemble cast than as a headliner.
That and we really need Iris. Iris West is what kept Barry from just running away into the Speed Force when he got his powers. His love for her keeps him grounded. When he pushes his power, it's her voice that calls him back, that lets him ignore that black-clad figure that beckons him on ever faster. With the power of my editorial fiat, I'd require that any depiction of Barry's powers from his point of view would have the Black Flash lurking somewhere, maybe hidden maybe not, in the panel.
So that's why Flash spends most of his time zooming around Central City splitting his time between Iris, being a CSI, and fighting the likes of Captain Cold, Captain Boomerang, Mirror Master, and the rest of the Rogues. For him to do more, to fight world-level threats like Brainiac or Mongol, is to risk sacrificing himself to the Speed Force. There are other speedsters in the Drewniverse, but none with real access to the Force (think sugar vs splenda - close but not quite). For example, Professor Zoom arrives from the future via a synthetic Speed Force he developed. He wants the Real Thing and through his attempts to usurp the mantle from Barry ends up teaching the hero a lot about the true nature of his powers. When Barry learns that holding onto the Speed Force is damaging the universe (an exaggeration on Zoom's part, but hey), he confronts the Black Flash for the first time (rather than just trying to ignore him as he normally does) and ends up striking a deal that will lead to Wally West getting speed powers like his uncle. Barry gets to feel like he's not helping to destroy the universe by refusing to run into the light, and Black Flash/Speed Force gets a crack at actually propagating itself.
As for the rest of Flash's adventures, we'll have to work hard to keep his power creep tamped down. We'll leave the Time Treadmill parked in the garage and keep walking between universes to a bare minimum. He'll get his own title (12/52) and will appear in team-ups (Flash is faster than Superman) and whatever form the Justice League ends up taking, but he will not be allowed to be used as a hand-wavey "er, uh, Flash fixed it with the Speed Force?" escape clause for when big cross-over events get out of hand.
Because thanks to Flashpoint, that well's done run dry.
Heh. Run. I'm so clever.