With protean and Greninja's great speed, you can immediately give yourself a handy resistance. Rahat is right; the bulkier eeveelutions like Sylveon, Umbreon, Glaceon, and Vaporeon will serve you best. Sylveon would probably be your best bet. His high special bulk, along with his handy resistance to fighting type moves (which Greninja is weak to) could help you out. Umbreon is who I would ultimatly use, however. The dual dark type thing wouldn't be much of a problem with protean, and umbreon's great bulk, as well as access to pursuit (greninja will probably force a switch or two) will help. Alternatively, You could match one of the faster "sweep-vees" (Jolteon, Espeon) with Greninja that knows a move that resists his partner's counter. Dark for espeon, flying for jolteon.