I would go with...
Aerodactyl:My ride. That thing would be frickin' terrifying to face.
Scizor, Marowak, and Infernape:Front line assault.
Zoroark, Dugtrio, and Ninjask:Stealth and flanking support.
Tyranitar, Mamoswine, and Metagross:Heavy hitters.
Goruggo, Bronzong, and Snorlax:Tanks to wall opposing attacks.
Blissey, Gardevoir, and Mamanbou:Clerics.
Flygon, Skarmory, and Charizard:Aerial support.
Starmie, Gengar, and Jolteon:Long range snipers.
Lapras and Wailord:Water transport carriers.
And finally, a lone, powerful Lucario to tear through the enemy ranks.
I'm an RTS fan. Sue me.