Firstly, the obvious PrC this calls for:
"Bartender"/"Dealer" aka Alchemist/Bard combo ;-)
And I almost want to see an Alignment: Chaotic requirement...
(though making them Chaotic only while "Transformed" would be even better)
Question: They get Craft (any) as a Class Skill and they can use spell trigger items if said spell is on Alchemy list... Can they Craft magic items if pre-req spells are on the Alchemy list? Perhaps the items only work for themselves unless they take the Infusion Discovery?
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I'm fine enough with most of the Alchemist formulae/infusions being magic-equivalent, including dispellable by magic... But having the Alchemist pop his Infusion of Giant Form just to have it be dispelled seems frustrating because he ends up barely distinguished from a generic Caster in the end, beyond his "Spell List" uniquely crossing Arcane and Divine spells.
I think playing up the Dr. Jekyll/Mr. Hyde "transformation" bit and giving them a Supernatural "Freakshape" Ability akin to Wildshape (but into Monstrous Humanoids?) would be great for the class, especially since alot of their abilities seem like they would play out as a pseudo-Arcane analog to Druids, with buffs/ transformations and control/ AoE damage (Bombs). (they really seem like the 'anti-Druid' thematically, so ability corellations like this make alot of sense)
Such "transformations" as currently enabled by the "X Shape" spell-infusions seem much more THEMATICALLY linked to the MUTAGEN Class Feature, and if Druid WIldshape is a standard of reference, should like-wise be non-dispellable. Why do Druids get Wildshape (Su) after all, and not just Bonus Slots for Animal Shape X?
I've felt similarly for other classes (specifically Elemental Bloodlines/Foci) but those were specific 'paths/ specializations' amongst other options that WEREN'T obvious corespondants of Wildshape - This is nearly the WHOLE focus of the class, so I think the case is 10x as strong here for such mechanical equivalence. The Mutagen bonus by itself doensn't really seem strong enough to bring a Medium BAB/HD class (w/ Simple Weapons!) up to par melee-wise like Wildshaping is for Druids: Why not wrap up (scaling) Monstrous Attacks/Abilities with the Stat Bonus all in one, since that's obviously how they would be used viably? Why penalize them (action/time-wise) for being a degenerate junkie anti-Druid? :-)
DIFFERENCES (vs. Wildshape) for such a "Freakshape" (beyond Monstrous Humanoid - or other - forms) could include specific PENALTIES while Freakshaped (given Monstrous Humanoid forms wouldn't have the inherent penalties of non-humanoid form to deal with). Penalties to Charisma (but bonus to Intimidate?), penalties to INT (though not affecting infusions/Alchemist class features), Rage-like limitations, etc. all seem viable and flavorful. Maybe along with INT penalty, the normal INT bonus could SUBSTITUTE for STR/DEX/CON while in this form (counting as Polymorph/Size Bonus, so not stacking with Polymorph effect, but perhaps making the net bonuses better than Wildshaped Druids, given it seems more of a core class feature for Alchemists...?) I mention the Simple Weapon Proficiency for a Class with Melee-Stat buffs as Core focus - Why not grant the Melee sibling of Throw Anything, "Catch Off-Guard", as a Bonus Feat while in this "Freakshape" form?