The text doesn't match the table for the # of abilities known, readied, etc.
That would be because I just changed them and I am bad at thinking through the ramifications of things like that. Give me a minute or so and I'll correct it.
How would this class interact with PrCs that stack for martial adept abilities?
Technically speaking, a sublime shaper's initiator level and shaper level are distinct. A prestige class that advances martial adept abilities
only advances martial adept abilities, while a prestige class that advances spellshaping abilities
only advances spellshaping abilities. Granted, you'll still get the 1/2 level increase to your unadvanced side, but that would be true no matter class you took levels in.
The more confusing question comes up when we get into the matter of prestige class levels that give you an extra maneuver readied or formula prepared. My ruling would be that you get an extra readied/prepared slot that can
only be used for the appropriate type of ability.
Anything I forgot to cover?