I have Mega Charizard Y and it seems that 99.9% of the time I am leveling him up his stats ALL go up by at least three if not four or five. The 0.01 Percent is when I forget to Mega Evolve him at the start of the battle.
Nope. Stats increasing upon levelling are determined by your Pokémon's base stats and EVs. Mega Evolution is not a factor.