I read a series of books once by Robin Hobbs (a woman) that was one of the best fantasy series I ever read. (Assassin's Apprentice, Royal Assassin, Assassin's Quest) ... and in those books the main character learns Alchemy for the purposes of assassination. It's very detailed, thorough, and was used to great benefit throughout the story, such that I (once having wondered how Alchemy ties to Thievery) saw all of the benefits to it. In fact, I think Bethesda should assign one of their game developers who is working on Alchemy to READ THOSE BOOKS for ideas. She pretty much masters the entire concept and as such I think those books would be the GO-TO books on the subject.
If Bethesda doesn't catch all the uses for Alchemy from those books, then perhaps a Modder could do it and add it in later....
Here are some uses I can think of:
I like these. If they could leverage the game engine to provide more interesting interactions and/or effects possible in alchemy, not merely limited the poison/potion dichotomy, then i think it would make the skill still useful even if the more power potion/poison effects have been nerfed.
The alchemy system in oblivion was deeper than any i've seen in any other game, but issues in addition to its high level balance problems made the system awkward and annoying at times. For example, the potion naming system was tedious, even if the basic name input is unchanged, i hope a new system would be more intelligent about organization and imeplentation to keep the entering of text to a minimum (perhaps a player-customized recipe book to easily recreate previous concoctions). I hope i can resonably expect to see good improvements to the alchemy sub-menu interface al well.
Here are some of my ideas for interesting aspects of alchemy, not seen in the vanilla games so far (i could not personally say if the same can be said for mods):
~Perhaps the Mages guild (or other magical organizations/shops) could offer amongst their services some sort of amchemy station or stationary alchemy equipment where you could make more powerful or perhaps more numerous potions than you could otherwise.
~Alchemy could be used in conjunction with the armorer/smithing skill to add enchantments or other improvements to armor or weapons that are not limited to the one-time-use poisons of Oblivion.
~Potions could be blessed at altars to gods (aedric or daedric) to improve their effectiveness or create unique effects (these could then be used as above with armors and the like to create your own legendary artifacts). you'd probably have to make significant offerings or perform some related side or unmarked quest to create these things. For example, the recipe for Daedric Lava Whiskey could be purchased from a follower of a daedric god and following a lengthy and complicated brewing process you could return to the diety's shrine to have it blessed and converted into its final state with amazing potency. It would be a great repeatable quest.
~Vendors or quest givers would make available potions with truly unique effects (think: conjuration or the scripted spell effects in Oblivion) that could be used in exaordinary circumstances or for very specific objectives (For example: a levitation potion, otherwise unheardof in Skyrim, is smuggled from Morrowind and is given to the player to complete an otherwise impossible thive's guild mission)
~Alchemy in Oblivion became very personalized once you were skilled in it, you built up a repitoire of often used effects and ingredients. Perhaps professional alchemists in Skyrim could be similar. You could even hear mention of such things in NPC conversations, "Felen Relas is truly a master at creating healing potions, the potions he sells are considerably better than anyone else's plus they cure you of disease and rid your body of poison." Ok, so it wouldn't be as canned as that dialogue (hopefully), but you get the idea. most merchants would have the standard selection of potions, but some would have ones that are more powerful or carry additional benefits/effects. The special versions would be more expensive and could be named after their creator so you'd know where to get more, "Felen Relas' panacea."
~Finally, as a simple matter of implementation, I'd like to see multi-step alchemy where ingredients must be mixed separately before being combined to create more powerful potions, recipes for such items could be occasionally found to help the player figure out the rules of the system before creating their own. Going further, perhaps recipes could call for parts of the concoction to be stewed over fire for a time before becoming viable. Such a mechanic would make the common fireplace or camp fire much more useful. Such things could be implemented as, or be part of, perks. like a master of alchemy can stew a single ingredient creating a single ingreditent potion which provides an interesting twist on the master perk from Oblivion.