My first thought on this project as a whole has been that the whole idea of TYPES of angels having a leader strikes me as implausible, since they are all supposed to be working together towards a common goal. I would have thought that "combined arms" would be the name of the game. Certainly it is in contrast to the fiendish leaders who DO have combined arms under them to one extent or another. I know I am VERY late in mentioning this, but you only now PMed me, and I don't ALWAYS give every thought I have when I glance at a thread. Note also that I could be completely wrong about this, and only some of the fluff would need to be changed, since the Angels DO specialize in certain tasks, so learning to fight in a way that uses heavenly power to imitate the methods of a given type of angel does make some sense... and oddly enough what I remember of the fluff (which I can't access since I am Away From Books and the SRD omits fluff I think), of the Core angels does tend to argue against combined arms.
Forge of the Spirit: Needs to be on the chart. I
would suggest combining it with Spirit Weapon, but I think breaking it up helps clarity.Make Spirit Weapon just a side chart, not listed on the level chart.
Did you really mean that imbuing a single Bite requires 110% of the cost of imbuing a Great-sword?
In the case of repairing a weapon, did you REALLY mean that the Ascendant can't get anyone else to do it for them? If so that is a dangerous trap if the person can't advance levels in the PRC, and has neglected to put any points into the requisite Craft skill.
Spirit Weapon: Again, upon actually opening this spoiler I think you should remove this from the class list, and just make it a reference table for Forge of the Spirit.
Transcendence: Can this stack with itself? I assume not. Note also that the DC is trivial to start out with. Was that intentional?
Astral State: Specify that the GM should roll the quest length secretly. Since they are meant to be about equally likely, just have it rolled on a d8 rather than d%.
What is the link between the base angel and animals, if any?
Eagle: Why a bonus on Grapple?
Shark: Can non-attack actions be mixed in-between attack actions? Note that this discourages full-attacks to a certain extent, which is opposed to the whole "shark frenzy" concept. Perhaps make it cumulative attacks that hit (just like you currently have), but make it only reset if you go a round without hitting the target, or hit another target (except with an AoO?).
Rat: You realize that anything with 10' reach satisfies this if you are medium or smaller and adjacent to it, right?
Spirit Projection: Needs Fluff.
Withstand: Since Evasion is a pre-requisite of the class, you need to reword this. something along the lines of "Evasion (or Improved Evasion) applies to this as well", also, since I think skill checks and saves work differently with regard to natural 1's and natural 20's you need to specify which way those work in this case.
Astral State: Still pretty easy to fix the ability score damage at those levels...
Instill Spirit Bond: Hmm... pretty cool ability... very dangerous to use since if they die, you do to... beward of high level leadership shenanigans with someone taking a member of this class as there cohort and then leaving themin a safe location after getting +8 to their BAB and Saves (you never capped the bonuses at the donator's bases, was that intentional?)
Shadow State: Probably WELL worth the Restoration , Greater scroll...
Spirit Warlord: Seems a little boring, but I assume it matches one of the abilities of the base Angel?
Feat: Very weak I think... maybe if you allowed it to be activated AFTER the result of the roll (including how much it failed or succeeded by) is known it would be worth it.