I was in the same boat (I played the genesis, or to be more accurate, MD version first). I actually got "suckered" into the cinema visuals of this game from one the first Japanese import mags that I bought, and subsequently paid an exorbitant amount ($80 or $90, can't recall...) to buy the import Mega Drive version of the game.
Years later, I played the PCE version, and PCE is for sure has the definitive version(s) of this game - if only because the cutscenes being one of the key selling points about this game, and by default the PCE/TG versions had the best cutscenes because of voices.
But anyway, the difficult water level NOT being in the Genesis weakens that version a bit more IMO. That's *definitely* the hardest single level in all of Valis series, and beating that level definitely ranks amongst the upper echelons of my classic gaming achievements.