my thought was better values for positive potions,lesser for spoiled and pure negative potions (drain fatigue etc).
While it's true that the game mechanics don't allow you to pour a potion on a weapon, in strictly role-playing terms, how would you define a purely negative potion? It seems to me that the whole concept of positive and negative effects is highly subjective. If I'm brewing a potion to use on my sick neighbor, cure disease is positive and drain health is negative. If I'm brewing a potion to kill the cave rats that are infesting my warehouse, damage health is positive and chameleon is negative. There are quite a few spoiled potions which are part of the base game, and their nature is obvious... they are spoiled. But there are also potions of burden, paralysis, and silence in the game, and they aren't considered spoiled. So obviously, they're intentionally negative. Which means there must be a use for them. Which means they have a value.
I do agree that potions could use a similar change in value, much like the enchanted items did. If there isn't an obvious or easy method of doing so with a mod, perhaps an overall reduction of potion values would be a good patch. I imagine something asymptotic so that strong potions are worth a great deal more than weak potions, but the insanely potent potions aren't really all that much more valuable because their usefulness is limited. After all, a potion that heals 50 health is a LOT more valuable than one that heals 5 health, but one that heals 50,000 health isn't really that much more valuable than one that heals 5,000 because nobody has that much health anyway. Beyond a certain potency, the benefits of a healing potion are mostly wasted, so it should stop increasing in value, or increase so slowly that the difference is practically negligible. The same is true of magicka regen, restore attribute, resistance, and even fortify potions. So the pricing curve for potions should be steep at low levels, but flatten out as the potency increases, and eventually practically flat-line so that potions above a certain potency simply don't get any more valuable.
I'm not sure what the asymptote should be, but the most valuable alchemy item in the game that isn't unique is Ancient Dagoth Brandy at 1500 gold and the most valuable potion that isn't rare or illegal is only 175 gold. I could see it being something in that range. Perhaps a fabulously potent potion might approach 1000 gold while a merely very strong one might hit 250-500.
For that matter, I wouldn't mind seeing an adjustment between the potency and duration of a potion. As it stands, when alchemy skill increases, both potency and duration increase quickly. It would make more sense to me if duration increased more quickly while potency increased less quickly. Which makes more sense? A potion that makes you 2400% resistant to normal diseases for half an hour or one that makes you 100% resistant to normal diseases for half a day?
My "dream" solution would be to find some way to allow the player to adjust potency vs duration with a slider in the potion maker. But since that looks to be entirely beyond even Hrnchamd's rather awesome abilities, shifting the emphasis from potency to duration would be a good compromise. And since potion durations don't stack like potency does, it would reduce the exploitation of potions for those who don't intend to exploit them while still leaving it possible for those who do. (To each his own - what doesn't harm my game doesn't offend me).