Just an idea I have: A series of smaller sourcebooks for fans of particular classes, much in the same way as the various "[Race]s of Golarion" books, but maybe a little bigger. Each one would go further in depth into each class, provide tips, and the like.
As an example, the first would likely be Ultimate Alchemist, as that comes first in Alphabetical Order.
After the usual introduction, a reprint of the basic information would be given. Followed by maybe a section on the history, development, treatment and roles of the Alchemist in Golarion. Following or alongside that would be a listing of all the archetypes (including new ones), what book they can be found in and a short summary of what makes them special (if you don't want a total reprint). The third section would be a listing of all their formulae (again, some new ones like maybe extracts based on debuffing/nerfing that could be used with the Infusion discovery), and various specialized equipment designed for Alchemists to use. Not just magic items, but more mundane things like variations of the Injection Spear that can draw fluids from a target (adding Bleed damage, for example, and allowing you to gather their blood/humours/etc...) or can be modified to spray their contents in a short 10/15-foot cone, that sprayer from Dungeoneer's Handbook, a heavy fluid gun with a hip- or back-pack reservoir (Flamethrowers ho! Forget that, Icethrowers ho!), a sling designed for hurling Bombs, and the like.
For more variety, new Archetypes, abilities, feats, or Formulas/Discoveries based on race can be added, like A Dwarven discovery that weakens stone (good for fighting golems or Elementals, but there's also the dreaded Dungeon Bypass).
Also maybe rules for adding their power to various Alchemical Tools and Weapons to make them more potent or allow whole new uses for them.
A big change I thought about is Multi-classing. To me, Multiclassing should be more than just dipping a level or two into a new pool for more abilities. Just as much as taking a single character class is a life choice for your character, taking a second should be just as important and defining. Whether as a series of traits, feats or abilities, or just roleplaying hints, these would be a few paragraphs (no more than half a page each IMO) about using the Alchemist class in conjunction with other classes in both concept and roleplaying. Perhaps an Alchemist/Monk, rather than just being a bomb-thrower who kicks people in the face when they get too close, is an aspiring Immortalist who uses Ki and meditation to refine extracts and mutagens within his own body as he seeks physical perfection. Or an Alchemist/Wizard who develops catalysts to increase the power of his spells/duplicate Metamagic effects.
Finally, there would be a few sample Alchemists. Damiel optional (after all, you may want to save him for NPC Codex 2).
That's about all I have off the top of my head. Suggestions, Ideas for other classes, etc...?