Flygon is one of my fave Pokemon ^^ I'd give it a Choice Band to increase the damage it can deal, and with Levitate, it can switch in easily to a Ground-type attack that they may have intended to use on Metagross, not to mention it also doesn't take damage from Electric-type moves, which would make it easy to switch into an Electric-type move as well, provided you scout for one first, since you have nothing that would attract one very well. I recommend giving Gallade protect to do this, since imo it's most likely to take an electric-type hit neutrally. It can also take Fire, Poison, and Rock easily, as it resists all of these attacks as well. With Flygon the only attacks you need to watch for are Dragons with a 2x weakness and Ice with a nasty 4x weakness. Luckily, Metagross and Infernape will be able to take those if you switch them into an attack. Lastly, remove Fly for Fire Punch, remove Crunch for U-Turn, and Dragon Claw for Outrage. Sadly, Flygon doesn't have a very diverse movepool and his Special Attack is really nothing to be proud of, so that's probably the best set he can have. Instead of this, you could attempt using a Muscle Band and use it for late-game sweep via Tailwind, but I think it would benefit more from the Choice Band's power.