Adding any resistance or weakness to water will require a deep analysis as 17% of the Pokemons are water type. If poison becomes super effective on water (what probably will not happen), not only the poison types will become more desired as well as poison type moves. It should be easy to defeat water Pokemons with poison instead grass or electric as water usually can cover grass weakness with ice and some of them can cover electric weakness with Earthquake/Dig.
In my viewpoint, I wouldn't like any other change in the type match-ups chart. It seems balanced since Generation and that's probably why they didn't alter anything ever since nor introduced any other type. And if poison should be super effective against water because living creatures cannot survive in polluted water, then we could discuss any other type match-ups that doesn't make sense. For example, fire shouldn't be super effective in steel because metals got high melting point. Therefore metalic-based Pokemons should resist to fire.