About the earlier concerns about Regular/Lowlight/Darkvision and light sources, here's how I deal with it: I fudge it. In dungeons, as long as someone in the party is carrying a torch/lantern or a light spell, I don't worry about illumination that much (and my dungeons tend to have lighting distributed around them). I generally presume that even creatures with Darkvision prefer at least modest lighting. When I describe the room, I describe it the same to everyone, unless there is something that could only be specifically seen with a special kind of vision (a long dark tunnel or deep hole and someone has darkvision). Generally, I presume that darkvision lets you get around in total darkness okay, but you get better detail and less eyestrain with at least a little light, low-light vision means you see A-OK in torchlight or other minor lightsources, and do just fine at night unless it's complete cloud cover and no other source of light. In practice, it rarely comes up since someone's got a light source (or at least a burnt out ioun stone with Continual Flame cast on it, so it's a cheap lightsource that doesn't take up a hand). Is it RAW? No, but it works and it keeps the game going just fine.
I've got no problem with D&D magic, magic items, monks, psionics, hit points, reflex saves, ect. That's just what D&D is. There are many other games out there that try and be more "dark and mysterious" or "realistic" or whatever, D&D is, IMO, over-the-top high fantasy that isn't supposed to be highly realistic.
The big thing from the RAW I couldn't stand is Favored Multiclassing. Why are Elves better Wizards than Rangers and Druids (which both seem more stereotypical), and why are Gnomes excellent Bards, when until a few years ago they couldn't even be bards? What I did was just ditch all multiclassing XP penalties and favored classes. To preserve the multiclassing advantage Humans and Half-Elves got, I gave them the "Adaptive Learning" special ability (from the UA Human Paragon class and d20 Star Wars Fringer Class), where they designate any one class skill they have at 1st character level as a permanent class skill, no matter how they multiclass in the future, so it only comes up if they multiclass, and only to a class that doesn't get their chosen skill, which still makes the Humans & Half-Elves the best multiclassers but doesn't penalize the Elf Ranger 1/Druid 5.
