Just finished skimming through it and I like a lot of what I see, although I already knew what to expect from this thread already.
I would say my only real 'complaints' about what I've read concerns the feat Precise Shot, and certain combat maneuvers.
I like how you went through and did a lot to remover taxes on characters, whether it be feats, skills, or wealth and I've always felt Precise Shot was, with Point Blank Shot as its prereq, a two feat tax on ranged characters to become effective in combat. Mind you, I like Point Blank Shot, I just don't care much for Precise shot. I understand this may just be a difference of opinion and preference when it comes to the cost of certain combat styles though, so I can understand why you may prefer keeping this in.
The only real problem I have with some of the combat maneuvers is that they still provoke opportunity attacks, and this mostly comes down to a sort of implied feat tax, because in my eyes the various Improved [Maneuver] feats combined with the opportunity attacks creates a situation where people might never use them unless they have the feat, which to me at least leads to people only using regular attacks. Again, maybe I haven't looked into this enough myself, but this is my impression given a first glance.
Other than that, I really love TB and it was certainly worth the wait.
As far as what I'd like to see, its mostly just 'extras' and nothing that is necessarily needed do to anything broken in the system.
The first is a warrior-mage class in the same vein as the other "half-caster" warrior classes, the ranger and paladin. The only reason I say this is because this is personally my favorite archetype, and until 4e, D&D has never really done this archetype any justice, in my opinion at least.
The only other thing I'd love to see is more feats. Lots more feats. Specifically higher level, 'advanced' combat feats, something that builds off the various improved combat maneuver feats. I also think it'd be neat if there were some feats that built off of the save boosting feats (lightning reflexes, iron will, and great fortitude) giving some interesting abilities thematically linked to each feat.
I understand though that such things are outside the scope of TB, but I can at least dream, right?