One way would be to tie the difficulty to the equipment, so you'd have 0 failure rate using the tools for your current skill level, some chance of failure if you used a step above, and no chance if you went 2 steps above. Making the results dependent on the tools (and bringing back the odds of success based on skill versus difficulty), rather than your character's skill, would place the "output" into neat "steps" like everything else in the game, and it could even STACK in inventory. Anything above "Master" or possibly "Secret Master" level wouldn't even exist, so you couldn't do the absolutely insane exploits like boosting your Strength by 1843 points for 428615 seconds. You could still make a "beginner's" spell that you could actually CAST (or a weak enchantment that would fit into a small item) from a "Journeyman" level spell that you were able to buy. The higher level tools could EXIST in the game from the start, rather than mysteriously appearing or replacing the more basic ones as you levelled, but they'd be of little use to you until your skills improved.
Another way would be to use a non-linear cost curve, so you could do basics easily and cheaply, but those "uber" spells, potions, and items would either cost a fortune in materials or have such a high casting cost that you effectively couldn't use them above a certain point (a "soft" cap).
Instead, they took some of these out of the game, yet added another, which is equally unbalanced. Duh? Obviously, "balance" is only a part of the reason for removing them, otherwise they'd have removed all or none.