Healing & Treasure
Besides Alchemy, you will need to increase the usefulness of the Healing skill, perhaps allowing a successful skill check to cure a small number of HP/wound. Also, institute a "Healing Herbs" system for use with Profession (Herbalist), and perhaps other forms of Medicine/Surgery usable with Profession (Apothecary), or somesuch.
For treasure, you can have alchemical and herbal remidies, instead of potions, and institute "superior" weapons and armor. Most forms of "Treasure" will be merely money, otherwise, and that quickly pales...
A new system for rewarding the players will have to be developed. Allies, Friends, Followers, etc., will need to become more important (especially as one person will be able to accomplish less). Superior technology will become more important. High skill will become paramount, as there will be no other way to overcome obstacles. "Antiabilities" (which stop other creature's powers from working, such as the Bard's ability to negate sonic attacks) will be pivotal in a few situations, but unimportant outside them. Firearms?