^Except if you attack with KGL they don't discard in between turns, Flygon's Body only works if it's active.
The main problem I can see with a KGL/Flygon combo is, well, ok, there's more than 1. They both require multiple energies (Or a DCE for Flygon) is the big one. Second, KGL doesn't boost Flygon's second attack, making Power Swing kind of power.... less... LOL Also, both a stage 2 and a legend are hard to set up, meaning you'll have to choose which one to set up first and just kind of hope the other comes together.
Honestly, I'm going to be running FlyKing next season. Slowking HGSS to choose which card your opponent discards from the top of their deck, Slowking Prime for draw power (It's not the same as Uxie X, but it boosts Flygon and I'm going to run a few Underground Expedition to make sure that if they drop a card I need I can get it back) and Flygon to be, well, Flygon. XD Early testing shows it works pretty well, one time against a SP deck I discards 3 Poketurns in a row.