>>56335305This is actually kinnda analogous to some cases irl, if an animal with high cost or tradeoff-heavy adaptations end up somewhere where they're no longer needed, they can eventually end up evolving out of it. Given the differences the environment in Johto must've been far less harsh than the waters of Hisui, thus giving it room to acclimate better to the aquatic environment (gaining the Water type) and getting rid of the evolutionary need to have a second stage (no longer evolves.
