I’m late to this particular party, but my chief gripe with both PrC appendices is that there are just way too many niche classes full stop. Take Elementalist and Element Master. Do we really need 2 separate 5 level classes that emulate the feel and abilities of 2E clerics? Redesign them both into one 5 level class, or else make a 10 level (Para/)Elemental Cleric PrC with all the abilities in. Same for Restorationist (which I like) and Earth Defender (which just feels redundant). Merge them.
Elven and Kreen PrCs…someone had a serious hard on for both these races. 7 PrCs apiece for elves and thri kreen. Get rid of the Desert Runner for starters. All elves are natural born runners and if a PC wants to max their running out there are feats and skills that do this already.
There are PrCs which just reflect a specific cultural view of things which don’t make a material difference. Magnus was a ‘Wind Singer’, ie: a cleric of elemental air. Stick him with cleric levels and a couple of redesigned elementalist/elemental master levels (as per above) and Bob’s your uncle. By my back of a fag packet calculation, you could probably reduce the contents by 1/4 to 1/3, freeing up space for some interesting PrCs that lean into other races and archetypes (dwarven PrCs for instance?).