Well, I looked at the Inno-Db stuff but a lot of it seem so be still in beta stage so to speak and not fully integrated with the rest of MySQL (e.g. you can't drop the DB, you have to drop each table individually).
Also, right off the bat they start talking about tablespaces and their maintenance, etc. and that's really one thing I don't want to do for an embedded app (reminds me of the nightmare that administering Oracle is).
An embdedded DB has to be self-running, zero-maintenance, self-recovering.
MySQL + Gemini seemed to fall into that category, but InnoDB might need some more work. I will look at it though, undoubtedly it's the direction the MYSQL team will go in the future...
Jacek