I like it, it's better than what I put together http://tiny.cc/i09ov
If possible, get the Table Number in the titles -- even if you have the title, the number comes in handy when trying to cross-reference into the book.
Some of the tables kind of disappear into the page in their last cell -- instead of alternating Color / no color, it might be worth alternating Color / off-white or light shading
Some of the abbreviations seem confusing -- since you made it I'm sure you know exactly what they mean but they take me a few moments when there's still a lot of white space.
I would shrink the size of the white internal margins and give the outside a bit more buffer for easier printing -- I'm guessing this was done in excel? shrink those interior margin columns.
While I kinda like the scattered color-coded layout, I would suggest maybe grouping tables a little differently (get most/all the "Skill use" tables onto one page, shift NPC and Environment entries to a single page (one that probably gets looked at less likely than the others))
I'd suggest aligning along the top rather than center-justifying the NPC Traits table
"PCs & villains can avoid assit. for 1 AD" -- take the extra couple lines of open space to make the text easier to understand at a glance.