I would be wary of many things if combining the material from the PHB and AU. Feats are either grossly powerful (for example, Speed Burst) or nearly useless. Combining them with PHB feats would make for taking the best of both worlds by ignoring feat chains. There are some crunch things that I think weren't considered deeply enough when it was put together, but hey, not even 3.0 was perfect right?
The magic system, while very interesting, has weaker spells than the PHB overall. The necessity of feats to gain access to complex and exotic spells is nifty, but makes for arcanists that have limited utility when compared to a wizard or cleric. Are they uniquely specialized? You bet, but I would also bet the majority have the same general arrangements to equal the PC power in the PHB, such as spending a feat to gain a 3rd level exotic spell to do actual damage.
Multiclassing would be the most overt abuse of the rules for each, as abilities from classes such as Witch when combined with a level of monk can get you an AC of +8 from Wisdom alone... at 2nd level. There are many more combos that could get out of line. The race levels are worth a warning as well, as they provide ability boosts and extras that make melee monsters that much worse, Giant in particular.
Within the AU rules alone I built a Giant 3/Warmain 6 that could easily have HP>100 and has large size with no restrictions on armor. Str=20, Con=20, and the damage output from weapons went up one size catagory. Taking a look at the casters of similar level with any build combos leaves them lacking versus melee builds.