Use these headlight buckets with some cool HID projectors. The further set the projectors are, the more alright it looks. I think Chaser Aero sells a replica.
Then put some kind of a lexan/plexiglass/clear cover over them, but make sure the cover extends all the way to the end of the bumper cutout, instead of just to where the pop-up headlight would end. And paint the bumper cutout to match the inside of the headlight.
Something similar to this, but less MS Painty. Instant Koenigsegg, McLaren F1, Dauer 962, or whatever supercar you want to pretend to be driving.
I have pondered flush-mounted headlights before, but arrived at the conclusion that the only way it will ever look as good/better than stock is if you can make them appear as if they could have come on the car from the factory. Otherwise something about them will always look off.