Charizard, Butterfree, Pidgeotto, Pidgeot, Fearow, Zubat, Golbat, Gastly, Haunter, Scyther, Gyarados, Aerodactyl, Articuno, Zapdos, Moltres, Dragonite, Noctowl, Ledyba, Ledian, Crobat, Togetic, Xatu, Hoppip, Skiploom, Jumpluff, Yanma, Gligar, Mantine, Skarmory, Beautifly, Swellow, Wingull, Pelipper, Masquerain, Ninjask, Vibrava, Flygon, Swablu, Altaria, Solrock, Lunatone, Duskull, Tropius, Chimecho, Staravia, Staraptor, Mothim, Combee, Vespiquen, Drifloon, Drifblim, Honchkrow, Chingling, Bronzor, Bronzong, Carnivine, Mantyke, Togekiss, Yanmega, Gliscor, Rotom (all forms), Tranquil, Unfezant, Woobat, Swoobat, Sigilyph, Archeops, Swanna, Emolga, Cryogonal, Braviary, Mandibuzz, Hydreigon, Fletchinder, Talonflame, Vivillon, Noibat and Noivern are all of the Pokémon obtainable in X/Y that can be used in Sky Battles.
Source: Sky Battles, Unobtainable Pokémon.