How about treating the Alchemist almost exactly like the Wizard class? Instead of spells, they get the equivalent Alchemical Formulae. They keep the formula in a book and get new ones at the same rate that Wizards gain new spells. You could treat the save DC the same way as the save vs. a Wizard's spell is determined rather than just a fixed Fortitude save. Plus this could increase variety in saves and such too.
Instead of always a fixed Fort save, maybe a Fighter needs to make a Reflex save after stepping on a "landmine" that is actually a ceramic shell with two chemicals in it that when mixed explode like a Fireball. A Rogue could wander into a dusty room that isn't filled with dust but an aerosol that makes those that breathe it more susceptible to suggestion and he has to make a Will save when he comes across the BBEG.
Treat different types of alchemy like the different schools of magic. Of course, this is up to your interpretation what these types would be but you could start with:
--Healing: This covers the Cure Wounds spells and other restoratives like Neutralize Poison, Remove Disease, Restoration, etc.
--Hallucinagens (?): This covers effects of spells in the Illusion/Phantasm area.
--Fortifiers: Covering effects that increase stats or improve conditions or resistances such as Bull's Strength, Resistance, etc.
--Mind Altering: Covers effects from Enchantment/Charm.
--Explosives: Covers effects from the Evocation school.
--Allergens: Duplicates effects from the Abjuration school.
--Lures: Produce a scent or sound that lures nearby monsters as per any Summoning spell.
--Drugs: May or may not relieve conditions or provide some short term effect or immunity but involve risk of addiction, may duplicate effects from necromantic spells.
--Poisons: We know what these are and the formula for them would be different for each type of poison and possibly for the reproduction of some debilitative magical effects.
--Transformative: Covering the transmutating effects like Alter Self, Polymorph, etc.
I''m sure there are other possibilities, but using these as a frame and the Wizard class as a foundation, you could create viable alchemists.
Not every alchemist would be familiar with every possible application either. Have the alchemist select one of the above types to start and then give them either access to another type every 3-4 levels, or let them learn extra formula of a type they already know. Someone who focuses on mind altering formula would know a lot of different possibilities at the expense of knowing how to make drugs or poisons or healing compounds.
And like how the Wizard can cast a number of spells per day, the Alchemist can create a number of potions or compounds each day, selected from the formula list that the Alchemist knows. Where a 3rd level Wizard can cast two 1st and one 2nd level spell each day, a 3rd level Alchemist would have the ingredients to create two 1st level potions and one 2nd level potion each day.
If you are going to allow Alchemists their way though, you may need to change the rules regarding immunity to poisons and instead change such immunity to a resistance and drastically increase the price of items that provide such immunity. Or maybe just strictly interpret immunity to poison as just limited to poisons, but drugs, mind altering compounds and things from other 'schools' above would work normally.
