OK, that document is bigger than I can get into right now and frankly a bit large in general for soliciting non-specific feedback. That said it looked interesting enough that I'll probably poke at it later when I have more time.
Observations from the first few pages:
The introduction that tells me 'what' I'm doing in the game should also give me some context for that. Fantasy, Historic, Sci-Fi, etc. OR specify that the game is meant to be used in multiple setting type to be decided by the group. I got as far as Phenotype and Races and thought I would get a clue there, but all I have are proper nouns by which to identify the 'races' but no description to tell me what they are. This information should ideally be introduced up front for a document presented to folk unfamiliar with your game or its terms.
I hate exploding dice, but I kinda like what you are doing by combining exploding dice (crits) with disappearing dice (botches). Size of dice pools and playtesting will determine whether it's brilliant, meh, or disastrous, but I like the concept enough that I would continue to work to make it work in some format if the initial testing doesn't go smooth.