This is perfect timing, for me, honestly. I just got into FMA (watching FMA:B currently) about 2 weeks back, and was thinking of making my own brew relating to it. Anyways, criticism time!

Expanded Spell List
I like the spell list, but Blight is already a Warlock spell.

Bonus Cantrips
Not bad at all. Could be nice to let shillelagh target gloves or gauntlets or something, to mimic some stuff in the anime, but it doesn't need that.

Certified State Alchemist
Looks good to me.

Equivalent Exchange
Looks real nice.

Return to Dust
I honestly really like this feature. I don't think it's unbalanced or anything, either.

Philosopher's Stone
Very nice, and very interesting.

Honestly, the only criticism I'd give this is that it doesn't really fit how warlock subclasses are officially designed (such as 10th level feature being more defensive), but I don't think sticking specifically to the way they're officially done is always a good idea. I'd totally use this.