Actually, Genesect can learn Fly... maybe that would be more fun, partly since it looks like it wouldn't be able to fly. Otherwise, I might take to the sky on a Skarmory (with a comfortable cushion on its back, of course). They're fairly large and, according to the dex entry, are very fast.
For a legend, I'd pick Rayquaza. Just the view of everything from the Ozone, and the solitude on the Sky Tower...what a sight...And for any regular ol' Pokemon, I'm gonna have to go with Flygon. It just seems so powerful, yet so elegant...
A Latios would be divine. He's probably among the most skilled and hardy of them all. We would be pretty close to where Rayquaza could get. Not to mention his battling capabilities. My first choice.
A Togekiss would be graceful. They're always reliable and sturdy when flying. Also, Togekiss are close to being legendary by my standards.
An oversized Scyther would be insane. Nobody in the sky would expect to look to their side and see a giant ninja mantis staring back.
Flying on a scyther sounds a bit risky to me. it's flapping wings seem like they could hit you. So it seems the dragon and legendaries seem quite popular. Ditto and its transform ability will be the best. could transform into any flying pokemon you want.