I have some suggestions:
Magic:
Make it hurt. A Fort DC equal to 15+Spell Level. If fail it deals 1d6 of real damage, if succeed it deals subdual. Makes for a "taxing" system.
Gods/Divinity
Kill the gods off. All of them. This correspondingly gets rid of clerics and makes games MUCH more deadly. Acknowledge, however, that clerics USED to exist; that way you still have all of those cool magic items
Creatures
No set alignments for any creature. ANY race or creature has a chance to be good or evil.
NPC's
Detail some humanoid adventuring parties, sponsored by the Local Dungeon Workers #205. 2 Orcan Barbarians, a Hobgoblin Fighter, a Goblin Rogue, a Kobold Sorceror, all banded together to ferret out the plague of light serving humanity. They would waltz into towns at night, going house to house, slaughtering everything and stealing all the valuables.
Another Side Note
mmadsen if you are seriously contemplating turning this into a book, I would be more than willing to help you out in the writing and expansion of ideas. I know how difficult it is to take a list or outline and turn it into pages of text. If you are interested in a partnership or anything let me know. I have spent a few years doing course design and development, I am used to my customers coming to me with a list of ideas and wanting it turned into an actual textbook and training course.