What if they usually did different things? Make the magical seem more magical, and the potions seem more body related. For example, light and night eye. I'd say a magical floating light should just be an illusion spell, but the alchemical solution would be night eye. You can do something similar between them, but there's enough space to make them worthwhile choices still.
Healing potions are over-used in my opinion, how about having them work over time instead of instantly? That way the magic can still work instantly, but there is an alchemical solution. What about cure disease potions? Wouldn't it be better if only potions could cure diseases, and restoration couldn't be that specific? It's better to have the fortify health ability with a potion than with a spell, but it's better to have a frost shield with a spell than a potion.
So generally, do you agree that separating spell effects from potion effects could make the potions more valuable? There needs to be much refinement I'm sure. Suggest other things in relation to potions if you have them.