Actually, Scarf Keldeo takes the moves that Greninja, a solid check for Mega Latias, uses against Latias very well. Keldeo doesn't care about Ice Beam or Dark Pulse, and SS is super effective against those Protean types defensively. Cobalion really doesn't like Low Kick Greninja or HP Fire Greninja, both common options.Scarf keldeo is also good, but gets worn down quick and will struggle to beat the darks throughout the game. Keldeo would work better on an offensive team, while coballion is rly good on balanced. But seriously, i am with you, i think mega latias is too much for the meta.
252 SpA Life Orb Protean Greninja Hidden Power Fire vs. 0 HP / 0 SpD Cobalion: 283-338 (87.6 - 104.6%) -- 25% chance to OHKO
0 Atk Life Orb Protean Greninja Low Kick (120 BP) vs. 0 HP / 4 Def Cobalion: 260-307 (80.4 - 95%) -- guaranteed 2HKO after Leftovers recovery
Dark Pulse Ninja especially gives the MLatias+Cobalion core fits, Scarf Keldeo is one of the best answers to Greninja out there now that Extrasensory Ninja is a relic. Cobalion handles Bisharp better, but Scarf Keldeo also handles it well.