Alchemy is a tricky one...
I am sure they left it out, because it opens some cans of worms. If you just use a skill (and ingredients), you can practically get magic without having the several skills/MP/dedicated POW yourself. Of course you could not duplicate many spells, but all those pertaining to the body (all healing spells, transmutations and enhancements) and some of the environmental things (transmuting one material into another e.g.) are viable. There are also several other options like the elixir of youth, the poisons, drugs, medicine and miscellaneous stuff (greek fire, porcelain, improvements like hardening armor, etc.) which need to be covered by the alchemy rules.
My answer to the thing in would be to have a set of alchemy skills: Alchemy (potions), Alchemy (materials), Alchemy (medicine), and so on. The effect of a concoction is determined on the sorcery table using the skill in question. The material determines the maximum effect anything can do (using troll blood for healing potions is good, using that of a hydra is better). By giving the ingredients values you can keep control about an alchemist running wild (some of the stuff must also be fresh, collected at a certain time, and so on...besides that this was done during our own dark ages, it is also a good way to make sure the PC alchemist has to get his stuff himself instead of buying it by the ton on the market before settling down to get industrialized). You do not have to write up all stuff in advance, but set a lower and a upper limit and fit stuff between that when it comes up (it is only important to know in advance what the limit will be and then make sure to never cross the line; e.g. to make greek fire you have to use at least petroleum (1) and the best basis would be fire demon blood (10), everything else like dragons blood would get somewhere between).
Second all products which are downright magical (like shapechanging, granting inhuman stats, full healing, etc.) require the alchemist to sacrifice POW similar to an enchantment.
You have also to determine the length of time it takes to make a potion or a batch thereof.
All of that stuff should tie in with the game world. People are supposed to be able to afford an alchemists products (otherwise he is out of business), but they *are* usually expensive. So you must find a formula how to price the stuff too.
The whole theme of alchemy can fill books by itself - and already did on the d20 license - if you want to do it right, and this is probably the main reason it got skipped so far.
I will for myself use houserules for it, based upon my d20 book (I bought it after all and most of it is not dependent on the rule system). I have had houserules on alchemy for AD&D and RQ 3 and it worked well.
(My players still remember fondly after 14 years the NPC alchemist they encountered first in RQ, when they wanted to find out about where to buy potions, what they cost and how many where for sale. After meeting him and seeing his workshop and what passes there for everyday life they decided to leave alchemy alone (it didnt keep them from doing deals with him

) and never argued about prices and availability. So I count him a success, at least for RP purposes
