Putting in a new proposal, one that might got shot down instantly due to being a blatant example of buff culture, but might as well try.
This is the current description for Water Stone:
While Poliwrath, Vaporeon, Ludi, and Simipour and their pre-evos can use the item to boost their abilities, it does absolutely NOTHING for Shellder, Cloyster, Staryu, and Starmie outside of raising their Def/SpA by one rank.
To counter this, I propose that Water Stone also buffs Shell Armor and Natural Cure (both abilities only one Water Stone mon has) so that Cloyster and Starmie aren't gyped with their signature item. I'm not 100% sure what the buffs would be, but I believe it certainly warrants discussion. Personally, I believe that a reasonable thing would be making Shell Armor act as a pseudo-Sturdy with Water Stone and making Natural Cure activate every round instead of every other round. I might be setting the bar too high with these suggestions, but they're mostly a starting point tbqh.