Charizard's in the game because transformations are gone and it's the most popular of Pokémon Trainer's Pokémon, and Greninja is in the game presumably because it's the most popular gen six Pokémon. The fact that they're both starters is likely only coincidental. Outside of fulfilling some imaginary "grass starter" niche, Sceptile doesn't stand out on its own. It's far from the most popular/promoted gen three Pokémon -- it's not even the most popular gen three starter (Blaziken is). It would stick out like a sore thumb among the playable Pokémon characters.