...Yes, that was what Thunder Wave and any reserves of excess cash were for.

Besides, Alakazam fell over when hit with strong physical-element attacks. As for the primary users of Psychic-types, Sabrina hardly qualified as a game-breaker, and Gary's Alakazam could be dispatched with a bit of battering. Squishy Mages at their finest.

Mewtwo may have been game-breaking in battle, but as you never fought any Mewtwo-users in-game and you were provided with the Master Ball to claim the prize itself, that seems irrelevant.