Class Skills: Alchemists already get Knowledge Nature.
Natural Remedies: Is his bonus formula from the Druid spells list in addition to his standard additions? Because, as written, when the alchemist gains a level he MUST select a druid spell instead of his own...which is silly.
Toxic Bombs: POISON! POISON EVERYWHERE! Actually, this ability is kind of on the weak end. It consumes his move action and his limited (and expensive) supply of poison. Consider just allowing the alchemist to add a dos as part of the standard action to throw a bomb. Or maybe create a discovery that lets him do it.
Natural Affinity: Add the bonus to Survival too to make up for only gaining one class skill and losing two.
Tailored Toxin: Now this guy is such being mean. He's only giving poison to certain people. That's favoritism. That being said, this ability is also pretty weak. I think you should either increase the bonus marginally, say one per 3 levels, or mimic this after the Precise Bombs discovery, in which the apothecary can choose squares that are exempt from his poison...unless, of course, this guy is supposed to have a fun-loving personality in which even allies are not immune to being poisoned, then ignore this recommendation.
Class Skills/Natural Affinity: You're right, of course. I think I just missed that in reading the list. That means I can mess with natural affinity as well. I like the idea of dropping the addition of Local and giving him a bonus to Survival and Nature.
Natural Remedies: Yeah, it looks like that got lost somewhere between my drafts and putting it up here. It's supposed to be in addition to the normal alchemist formulae.
Toxic Bombs: I think the original reasoning for using a move action was to limit it to not being affected by things like Fast Bomb, but now that you point it out, that line of reasoning is a little off. I'll go with just doing it as part of the bomb creation.
Tailored Toxin: My original idea for this was giving his allies a cumulative 1% chance per however many levels to not be affected, but that seemed a little odd for some reason I don't remember. I'm tempted to make it similar to the alchemist's poison resistance in that it grants an increasing static bonus, then caps with immunity. How does that sound?
Edit: Here's the whole thing with all mentioned changes.
More in touch with power found in nature, apothecaries excel at creating natural remedies for bolstering allies and subtle poisons for those who cross them.
Natural Remedies (Su): Each time an apothecary adds new formulae to his formula book for gaining a level, he selects a single spell from the druid spell list with a target of personal or touch with a spell level less than or equal to the highest level of formula the apothecary is capable of using. He adds this spell as a formula, using his Intelligence modifier in place of his Wisdom modifier, and his apothecary level as his caster level. This is in addition to the normal alchemist formulae gained. Because of this training, however, his offensive potential is lower. His bombs are reduced to 1d4 damage, plus 1d4 damage for every odd-numbered level instead of 1d6.
This otherwise functions as and replaces the standard alchemist alchemy and bomb class features.
Toxic Bombs (Su): As part of the action to create a bomb, an apothecary may add a dose of a contact or injury poison to a bomb. If a target takes damage from the bomb, the bomb and poison affect the target normally. Those that take damage from the splash are also required to make a save against the poison, but at a +4 bonus, and are only affected by the primary effect.
This replaces the mutagen class ability (an apothecary cannot create a mutagen unless he selects the mutagen discovery).
Nature Affinity (Ex): An apothecary gains a bonus equal to 1/2 his apothecary level on Knowledge (nature) and Survival checks.
This replaces the 2nd-level discovery class feature.
Tailored Toxins (Ex): Starting at second level, an apothecary can make his poisons less dangerous to his allies. At 4th level, an apothecary's allies gains a +2 bonus on all saving throws against the apothecary's poisons. This bonus increases to +4 at 7th level, and then again to +6 at 10th level. At 12th level, an apothecary's allies are immune to an apothecary's poisons.
This replaces the 6th-level discovery class feature.
Discoveries: The following discoveries complement the apothecary: combine extracts, dilution, infusion, malignant poison, poison conversion, precise bombs.