Deck out Flygon tries to keep Wind Erosion out as constant as possible. It puts a lot of pressure on your opponent to get rid of the Lv. X ASAP. You can really do this with ANY Flygon deck... In my Flygon variants I've tried to keep at a lot of recovery cards in there. I ran one with 2 Night Maintenance and 2 Premiere Ball... and while it can yield some dead draws I think it pays off. Once Flygon Lv. X hits the field it's really hard to get around discards except one of the few turns you KO it... and Warp Points sometimes do the trick (This may save a discard but you (Usually) can't hit Flygon, so it's sort of a trade-off) also but in both of these cases you're only saving yourself from 1 of the 2 in-between-turns discards.
Weavile is probably the most consistent "Straight Flygon" if you wanna make Flygon your main attacker. Mewtwo Lv. X is pretty much a win against SP decks, granted you get it out. You keep Mewtwo out while you charge up Flygon, then hit Dialga G Lv . X when it hits the field... So you'd probably attach to Flygon before Mewtwo and maybe Energy Absorbtion if you could. Ninetales is a tech that's becoming more common and can be played in things like Blaziken, Infernape, or Luxape variants to get past Mewtwo a lot easier than Dialga G Lv. X. Anything that has a good Poke-Body or is reliant on one is good to play with Flygon since you can get rid of Dialga G easily (Just like the Mewtwo concept, and Manectric and Nidoqueen work too). Dusknoir can be played in pretty much any Flygon build that has room since its almost never used as an attacker except in desperation if you play Psychic energies (Perhaps in a Mewtwo build), you'll usually only see it as a 1-0-1 line. Nidoqueen can be played in this fashion too if you don't plan on attacking all that often with it.
One thing that wasn't mentioned was Palkia Lv. X (GE), it has good synergy with Rainbow Float.