It seems to me that the innate abilities are present in this system as innates for two reasons:
1. To provide incentive against heavy splashing while the trees themselves are very multiclass friendly
They are placed as innates simply by assigning a progressively higher ML to progressively more powerful abilities (eg. ML:6, ML:12, ML:18, ML:20). The rules by which these abilities get their ML are different than the rest of the tree (which is: ability in a certain tier is available as long as you have that same amount of levels in the class).
2. To create an action point sink, since you need to acquire the lower tier abilities in order to gain the upper tier ones, assuming that the upper tier ones are highly desirable.
So, I submit to you, the developers, a question: Why would you create an innate line with sequential advancement, when the ML mechanic of the tree itself is already multiclass friendly?
This, in part, lies at the heart of the death of a lot of pure builds. There are many innate abilities that you are forcing us to take until we reach the capstone enhancements, that most of us say screw it. Then, we multiclass in order to compensate for losing that one capstone ability, simultaneously saving all the action points we otherwise would have spent toward that capstone. WIN.
My point is that the power of the capstone isn't solely responsible for the death of pure builds. Its the action point tax of the other innates, as well as the outright uselessness of them, that deter people from purity.
My wizard does not want every form out there in order to reach the capstone. My fighter does not want that silly spiritual bond thing or the vorpal strikes (since it shares a cooldown with a boost last I checked) so that I can grab my capstone. My halforc doesn't want that morale bonus to strength when his health gets low just so that I can grab a strength or even begin spending my points in the tree.
Divorce the innates from one another. I don't want them to be pre-reqs for each other, the ML suffices.
Don't FORCE me to spend my first point(s) in the first innate just so that I can open up the tree, I don't always want that first innate.