The title should be self-explanatory.
1. Typing advantage
Without Alain's Charizard in its mega form, Greninja has the type advantage of water over fire. However, remember that when Alain's Charizard mega evolves, it gains dragon-type characteristics. Due to water being only 1/2x effective against dragon, it would moderate the effectiveness of Greninja's attacks. Add to this the fact that Alain's Charizard knows Thunder Punch, a move that's super effective against Greninja, and suddenly the tides have turned.
2. Level
We don't know for sure how long Alain had his Charmander, but I think it's fair to assume that they knew each other longer than Ash and Greninja. Assuming that Greninja did indeed evolve at level 36 like his line is supposed to, due to the timing of his evolution it would probably be fair to assume that he was around level 50 or so by the start of the Kalos league, while Charizard was most likely around level 75 or higher. I don't care what you say; a level 50 Greninja is still going to get its ass stomped on by a level 75 Charizard. Hell, I've beaten grass-types in my Pokemon X game purely because my Greninja is level 100 and the Pokemon I was battling were all level 55 or lower.
3. Move power
Blast Burn has a power of 150, while Water Shuriken's power is only 15. This kind of relates to the other two reasons, because although Water Shuriken is a priority move, it still wouldn't do as much damage against a higher level Charizard, whereas a 150-power move can almost always knock out anything, especially if the opponent is at a lower level regardless of type advantage.
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Pokemon One-Shots and Headcanons
FanfictionJust a few one-shots of the Pokemon from XY. Told from all different perspectives. This is my first attempt at a Pokemon fic, so don't kill me.
