I'd simply have a shadowed figure in an alleyway or something wearing a vague yellow suit observing the Flash (at work) from afar, and just before the camera cuts, have the red eyes glow.
I've always envisioned a big screen Flash trilogy having Thawne as the big bad for the third film, but with him having an active role in the first two. An opener would introduce the rogues, and have them as the antihero/villainous group, being supplied anonymous information and tech from Thawne (unbeknown to them who it is).
A second film would have someone like Grodd as the villain, having been manipulated by Thawne to go after Barry. The third film would be Thawne himself, but I'd actually have the rogues assist Barry in some capacity in defeating Thawne; the comics have always alluded to a strange amount of respect between Flash and the Rogues, and I'd like to see that transition on the big screen.