Like many others, I've been looking forward to this mod for a long time so there would be an Alchemy mod that makes Alchemy a much more useful part of the game.
A few thoughts on the areas for debate:
Bombs: I would also put Shock bombs in the same category as fire bombs. Stun effects can be obtained using a mix of non-magical chemicals (usually including aluminum) and doesn't need gunpowder, and Corundum in the game has been likened to aluminum. The magic system includes runes which provide a bomb-like effect, so I could also see justifying bombs as the alchemical version of the magic runes.
Potions: Often the real effect of taking multiple doses of the same potion is diminished benefits for subsequent doses after the first dose and the increased possibility for significant side effects (typically harmful). Adding these two factors (diminished returns and the "poisoning" effect mentioned by Tech) might be difficult to add to the game. I feel non-stacking potions (for potions with the same effect), along with potions of different strength, is the best alternative without making a significant change to the scripts for potion use to accommodate both of these changes (I realize the new alcohol effects in CACO handle both of these, but it is a lot more complex than the ordinary potion effects). I don't think taking multiple copies of the same potion should increase its duration; taking more aspirin (as an example) doesn't change the duration of the effect.
I also feel that potions should not take effect instantly, and should provide an effect over some time period. Some would act very quickly while others would provide an effect (e.g., increasing health) at a fixed rate over a predetermined time. Some would provide an constant effect (e.g., improved weapon skill) over a period of time.
Needs: I agree that this should be up to the individual player. The Fallout 3 Wanderers Edition mod included the Needs mechanism in the Fallout series (based on an existing Fallout 3 mod) and Bethesda then included it in the vanilla Fallout New Vegas. In both cases it is optional. I like that CACO has tried to provide a lightweight Needs capability while retaining compatiblity with other Needs mod like iNeed (which I use).