Flygon's EVs said:
For the special sweeping set, make him Modest, Mild or Rash, but I'd go with Modest. Put everything you don't put in Speed in Special Attack, with a little leftover for Attack. Do the same for the Sunnybeaming set
Flygon does not have a sunnybeaming set
Also a few more countering stuff:
-Celebi makes a great non-CB Zapdos counter. HP Ice only does ~38% damage to it, and it can easily CM up in Zappy's face, and of course, if Zapdos has HP Grass, then Cele busts up Zappy without fear.
-Articuno is a fantastic Celebi and Non-Rock Slide Swampert counter. With an incredible Sp.Def, this will eat Swampert and Celebi out of PPs (If Celebi has Calm Mind, you can roar it away)
-Ariados is a great non HP Rock Breloom counter. 4x Resist to Fighting, immune to Spore, and has a Sludge Bomb to work with.
-I don't quite get how Deoxys-L is a Kyogre counter. I mean, if you switch into a CM, then deoxys-LOL gets 2hko'ed by Surf, while the most Deoxys-lol can do is Night Shade/Toxic/Thunder Wave/Knock off (and seeing how there are a number of 101 Sub Kyogres)