What about class abilities? I'm the sort that plays a lot of multiclasses, but with only 6 levels to play with I could see this being more difficult. (Not a knock against, merely a factor to be considered.) On the one hand, splitting classes might mean you lose access to a higher level class ability; if you go Fighter 4/Ranger 2, you'll never get an Animal Companion (for a really poor example). Rogues will never get Improved Uncanny Dodge, however a Rogue 4/Barbarian 2 would. (Also, just glancing at the progression it would seem like Rogue 6 would be pretty rare, all they get is Trap Sense +2; it seems like they'd be better off with almost any other class-- fighter for the feat, BAB and Fort, Sorcerer for the spells and Will, Barbarian for the Fort, BAB, HP, Rage and Fast Move, Monk for the Flurry, Saves, Imp Unarmed Strike and so on.) If you use feats from AE, which my group does, Uncanny Dodge exists as Intuitive Sense, so anybody would be able to pick it up. Wpn Specialization is in there too with just a +4 BAB, which would make it accessible to other classes.
I also notice that capping it at 6th means some characters might be eligible for one level of a PrC. It seems like an assassin's Death Attack would be a lot scarier in a world with capped Fort Saves. Horizon Walkers would be limited to one Terrain Mastery, but that actually makes a lot of sense.