A counter for this pokemon?
Mega Pinsir, Magic Guard Reuniclus, Magic Guard Sigilyph, Magic Guard Alakazam, Specs Latios (Psyshock/Psychic), Offensive Roserade (Extrasensory, Technician HP Flying), Talonflame, Tornadus-T, Kyurem-B, Acrobatics Gliscor, Hawlucha, Taunt Skarmory, etc.
Thing is Hidden Power can help Megasaur get past certain checks you'd think would counter outright. HP Rock for instance demolishes Char Y, so it absolutely can't switch into that, or it and Sludge Bomb.
252 SpA Mega Charizard Y Air Slash vs. 252 HP / 4 SpD Mega Venusaur: 242-288 (66.4 - 79.1%) -- guaranteed 2HKO
252 SpA Mega Charizard Y
Overheat vs. 252 HP / 4 SpD Thick Fat Mega Venusaur: 210-248 (57.6 - 68.1%) -- guaranteed 2HKO
252+ SpA Mega Venusaur Hidden Power Rock vs. 4 HP / 0 SpD Mega Charizard Y: 248-292 (83.2 - 97.9%) -- guaranteed OHKO after Stealth Rock
252 Atk Choice Band Talonflame Brave Bird vs. 252 HP / 252+ Def Mega Venusaur: 266-314 (73 - 86.2%) -- guaranteed 2HKO
252 SpA Mega Venusaur Hidden Power Rock vs. 4 HP / 0 SpD Talonflame: 340-404 (114 - 135.5%) -- guaranteed OHKO
While Heatran doesn't normally have anything to hurt Megasaur in particular, it can really cripple it through Burn from WoW or Lava Plume.
252 SpA Heatran Lava Plume vs. 252 HP / 4 SpD Thick Fat Mega Venusaur: 114-134 (31.3 - 36.8%) -- guaranteed 3HKO after burn damage
0- Atk burned Mega Venusaur Earthquake vs. 252 HP / 0 Def Heatran: 124-146 (32.1 - 37.8%) -- 0.2% chance to 3HKO after Leftovers recovery
That doesn't factor in Torment or Protect either. HP Ground on the other hand has no trouble with Timid versions and at least isn't weakened by Burn.
252 SpA Mega Venusaur Hidden Power Ground vs. 0 HP / 0 SpD Heatran: 240-284 (74.3 - 87.9%) -- guaranteed 2HKO after Leftovers recovery
None of these factor in Growth however, and I say if you're going to run a Hidden Power than you kind of want the Growth boost and run the mixed attacking set. One Growth changes many of these calcs considerably. OHKO on Char Y. OHKO on Heatran with Earthquake with Stealth Rock, clean 2HKO even if burned.