I would use Zoom in the first movie because he is such an Iconic Flash villain, Imagine Wally getting the crap kicked out of him by Zoom only to have Uncle Barry Rip through space and time to help in run the final race up Zoom's butt and take him down!
That way...Flash can fight the 1st Zoom in the second movie and the NEW Zoom and the OLD Zoom in the 3rd sorta like what Raimi did with the Green Goblins.
Eobard Thawne (Zoom I)
Hunter Zolomon (Zoom II)
That is a pretty good idea DarkSuperman. The Flash movies would definitely be a movie about legacy and they could have flash backs of Barry Allen and what he was all about. They could have Professor Zoom as one of the enemies in a flash back, and then have Hunter Zolomon be a metahuman profiler for the police, like in the comic, and be inspired through a tragedy to take the mantle of ZOOM to make Wally a better hero in his warped mind.
The distinction should made between where Professor Zoom and ZOOM's powers come from. ZOOM's power should be made more of a threat than Professor Zoom, because it is only gets more challenging in the later films. And you can then have Capt. Boomerang , Weather Wizard, Mirror Master, and Captain cold be reoccurring in the first 2 movies. I wouldn't get too involved with the back story of all of the rogues because it would take some time. Spider-Man 3 was all right, but it seemed like too much activity between Spiderman's personality changing due to the symbiote, Venom, Harry as the new Green Goblin, and the Sandman. I would also have Iron Heights in the movie to show how many rogues the Flash had locked up over the years. It would have to be a movie with more than one villain, but it works with the Flash if its handled like it is in the comics. The only exception would be the 3rd film, the only villain could just be ZOOM.