Whether you should use an Alpha or a regular Pokémon depends largely on your moveset.
Generally, it's better to use an Alpha when you make heavy use of area of effect moves that attack a radius around the user (like Earthquake) or moves that involve rushing the opponent using the user's body (like Waterfall), as the user's size affects the moves' hitboxes. Compare this with a move like Ice Beam or Earth Power, which causes your Pokémon to stand near its trainer and launch an attack from a distance. These moves don't benefit as much from increased body size, and being too tall might even make it harder to land beam/projectile attacks at certain angles, so Pokémon who rely on them might want to stick with smaller sizes to reduce their own hurtbox.
I don't know what set you're using—and that might be something you want to tweak over time—but as a broad recommendation, several of Greninja's top moves are ranged, so you're unlikely to get much out of extra size. This includes Water Shuriken, Hydro Pump, Dark Pulse, and Ice Beam. Additionally, Mega Greninja's bulk isn't the most amazing compared to some of the other megas in the game, so literally making yourself a bigger target might be challenging. But overall, since you have both Greninjas, you might just want to take some time testing out the moves you're interested in to compare the two of them. It's honestly not the biggest deal in the long run if your size is slightly suboptimal; skillful battle technique and good sets make a much bigger difference.
One last note is that you shouldn't really consider the default maxed out EVs in HP that Alphas come with. They're convenient, but seeing as you can EV train any regular Pokémon to match their bulk, they don't provide any actual advantage, especially since it's really easy to EV train or buy vitamins in this game.
