I like the idea of only allowing Alchemy at a static station. I have a love/hate relationship with alchemy in past TES games. On the one hand, it's extremely convenient. You can just brew up a potion for anything you need right there on the spot. Got hurt? Bam, health. Too much loot? Lemme just brew up some Feather. Oh this cave is flooded? Water breathing!
On the other hand, it's extremely convenient. You end up carrying around an entire pack mule full of ingredients. In my case, 1-10 of every ingredient in the game. It's rather ridiculous. It also encourages you to just spam gather everything in sight. Sure, I could not do this and pretend to only be able to alchemy at my home, but the game is kinda balanced around the notion that you can alchemy anywhere.
So I would very much like a system where you gather up ingredients, bring it back to your home/wherever, plop 'em in a chest, and then custom brew potions you think you might need for the next quest. To that end, I would like more hints in the quest journal. For example, if you're to kill a wizard in a den of conjurers, you'll brew up some shock/fire/frost shield and some silence poisons. If it's undead, some resist disease/cure disease and fire poisons (rather than damage health). You could still just end up brewing a potion for every occasion but by that point you've earned the right to be that tedious and thorough if you choose.
Another thing I'd like to see with alchemy. You can make potions with matching hidden effects, but those effects will be hidden until the potion is brewed. So, say, you have 2 hidden effects on ingredients. You want to make a healing potion, so you grab some Fancycap and Stickyweed. The Fancycap has effects as follows: Fortify Personality, Restore Health, ? (Light), ? (Damage Speed). The Stickyweed has effects as follows: Damage Speed, Restore Health, ? (Damage Willpower), ? (Frost Damage). You put the ingredients in and see in the output box "Restore Health 8 points for 10 seconds" and "??? This effect is unknown." You brew it up and... damn! A negative effect. Oh well.
It'd be nice if there were more books that told you "safe" recipes for some common potions. Not recipes, just in-game books with suggested ingredients.