Jeff's stuff:
As Jolly said, we ain't making more disciplines. Certainly we're not making another discipline that works almost identically to an existing one. What exactly makes it worse? There are disadvantages (loss of immunities, likely lower HP) and advantages (feats, not mindless). (On the not-mindless front, I clarified that they speak one of the elemental languages or Sylvan, and gave the arch those for free.)
I had planned to make them more distinct, by restricting some customizations and giving them access to evolutions, but on looking that list over they almost all center around making more or better natural attacks, which is not what I was going for with the automaton. In the end, they ended up being a different flavor of tinker that will play a little differently, and I'm okay with that.
That's fine; you don't have to. I personally will probably never play one. I like skill points and Knowledge skills too much. However, an alchemist with Charisma is equally valid. As examples, take the Sparks from Girl Genius. (Jolly also suggests Mei Hatsume and Miu Iruma. Not being familiar with their respective properties, though, I accept no accountability if they're off the mark.)
While Intelligence has something of an edge in inherent usefulness, it is simply wrong to say that it is flat-out better. Same thing with extracts vs. psychic spells. It's a trade off that's fantastic for some characters and players and absolutely wrong for others, which is exactly what I like to see in archetypes. In addition, the Legendary Alchemist has between 4 and 8 skill points per level before Intelligence (depending on arch and ACFs), which is plenty to play someone who both commands minions and blows things up.
(I did give it the social skills, though, as I realized that it didn't have the support to make good use of them.)
In addition to the changes noted above, I thought I'd mention that I've decided to nix the discovery gate in front of major and fantastical customizations. Thinking back to my original design work, it's a legacy from an earlier design paradigm we abandoned.
I also added language letting you use your unarmed strike in place of a slam for anything related to customize self.
And it now gets Knowledge (engineering). How the heck did the original class not have that?