Dr. Alchemy and Captain Boomerang.
I don't think you can do the Rogues in an origin movie because they need so much buy in. It needs an Incredibles flavor, as mentioned, but when you do that Incredibles tone in live action you get Scott Pilgrim. Great movies that the general audience 'doesn't get.'
You also can't do the Rogues in an origin film because you have personalities to establish, and you're in the middle of establishing a world, powerset and main character that's supposed to be engrossing for the audience. Take too much time away from that to develop your villains and you have a Green Lantern.
Dr. Alchemy as a science chemistry guy who has a friendship with Barry in the comics slides right into the origin quite nicely. We know CSI's don't have tons of weird chemicals, but cutting edge scientists do. Cue lightning.
Captain Boomerang not only requires no real explanation scientifically, but he makes for a pretty cool CSI case, and he can actually challenge the Flash, provided he has enough boomerangs.
I do like the idea of Zoom being behind the ubertech though. For the second movie villain, do a whole squad: Captain Cold, Heat Wave, Weather Wizard, Golden Glider and Pied Piper. Except Golden Glider isn't useless. Then end it off with Zoom, y'know?
Captain Boomerang could work if you don't call him Captain Boomerang (or maybe call him that once as a joke). I can see a lot of fights involving dodging razor boomerangs and explosive ones. Thing of the scene where Spider-man was dodging the razor pumpkin bombs. Maybe heat seeking boomerangs would work. He cannot work as a main villain, though. He has to work in conjunction with somebody else.
I always liked that the rogues were regular thugs but because of The Flash's presence and ability to be everywhere at once actually had to evolve methods to commit their crimes and keep safe. It's pretty brilliant and always something I wanted to see done in the movies.
I like the idea but I'm not sure how to make that a movie where Flash is the most interesting. It's a heist flick, but no one cares to see how they're caught. It's the planning of the crime that interest people.
I think something can be made out of that. This group of thugs are hired to steal something but it's never revealed who hires them. They're supplied with the technology to incapacitate The Flash should he get in their way. Movie goes on and they're taken out one by one and it APPEARS that they've failed but maybe someone like Mirror Master managed to escape using a copy or a reflection and gets the object to their benefactor. The benefactor turns out to be Zoom who needs the device for some reason or another.
This is just stuff off the top of my head. In a sequel maybe they can mix the two Zooms (since I doubt Hunter Zolomon will appear in the series if Barry Allen is The Flash) and say that this Zoom needs the device to stabilize himself in the time stream because he has trouble controlling his speed. The movie climaxes with The Flash and Zoom fighting around the world and through time.
This is just me brainstorming off of your heist idea, though.
I guess one of the bigger questions would be what exactly is at stake in regards to a final battle? They're just crooks trying to make a living in a sense, not trying to destroy the city or take it over. I don't know if they'd pull a Hancock where the actual antagonist is kind of him having to deal with what he's been given, and maybe just having a bunch of crazies running rampant in the city.
I like the idea but I'm not sure how to make that a movie where Flash is the most interesting. It's a heist flick, but no one cares to see how they're caught. It's the planning of the crime that interest people.