There was a homebrew FMA Alchemist class on the Gleemax forums that was pretty interesting, good luck finding it now though after the latest forum reshuffle.
Personally I'd make it a mostly transmuter Sorcerer, with the RP flair of drawing glyphs on everything as focus for my casting. If you're actually trying to build Ed himself, Automail would be an item rather than a class ability, a gauntlet with a hidden blade and some other nifty tricks would be your main melee weapon. (Yeah, I know, Sorcerer's not all that good for melee, and you'd need to spend a feat to be proficient... it's not a most optimal build, I'm aware.)
Most of the weird stuff those Alchemists do can be pulled off with transmutation spells with a little imagination and a DM willing to roll with the punches.
I think a psion would work, but battle sorcerer who focuses on transmutation spells could work(Proficiency with 1 martial weapon[Klar?], armor proficiency, d8s for HD, and the same bab as a cleric).
Gestalt (It's not as powerful as one thinks) (yeah you may be 2 builds in one, but you have to split your resources between each thus weakening the power granted by versatility)
Spell recharge (spells recharge over time. recharge rate is variable. best to treat all wands as eternal wands)
Power components (Free metamagic on the fly if you have the right goods)
Prestigious hybrid classes
Water Orcs
and a bunch of houserules ripped off from various other systems. such as action points, taint, and sanity.
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