Stacking potions would help, but the best choice would still be to leave potions on the floor until you need them. If you don't pick up any potions, then if you happen to drink the ones you have in the course of surviving the dungeon then you can replace them with something else until you need more. It won't happen that often, but it still creates a situation where there's an upside and no downside to hoarding. Even if you don't use up all of your potions, allowing for the option that you will use up a single type would allow you to carry an extra wisp amulet or other small item.
I guess the real question should be what is added to the game by having potions take up inventory slots. We know it detracts something from the game because it encourages leaving potions on the ground.
One option might be to have an inventory item called a potion kit which is required to pick up potions, but once you have it you can carry all you want. This should completely eliminate all hoarding while still making potions take up space. Or of course you could just go back to the way potions were carried in the freeware version, (where potions are just kept track of seperately at the top of the screen).