Another editing thing: you talk about Readied blemishes and Prepared blemishes at different points. I'd pick one term and use it consistently.
Also, would you consider a feat like Adaptive Style, to let blemishes be swapped faster than 10 minutes?
Adaptive Style feat...
Final Boss Form?
Nope, that would be a class feature for a PrC... Along with health bars.
As for the Martyr thing... I can see that as a Messiah-specific Blemish, probably working like shield other, but if the effect that's used on them allows a save, they both get to save, and:
If they both succeed: only the Messiah takes the partial effect.
If one fails: both take partial effect.
If both fail: Messiah takes full effect, other takes partial effect.
I'll have to think about that one...
And Shintais are... weird. I actually have to reconsider how I was going to work them, because they are really wonky as ACFs and don't really work as feats... And they don't work as Blemishes either...
Either PrCs, or maybe another Outcast class, that gets the ability to "cast" Shintais, which are a kind of pre-chosen set of Blemishes...
On a side note, I'm reworking Plague-Carriers Breath, and will be dropping Hunter's Venom; I just found the most amazing poison rework, and it is
glorious.