Here are some of my pet peeves:
Spellbooks – In additon to the issues that Rel mentioned: First they are waaaay too expensive. Each page requires 100 gp – that’s two pounds of gold – and yet they are just paper and ink. Second, they are completely useless to anyone but a wizard and even then, a wizard is better off scribing a copy into his own book because of the spellcraft check to learn from another’s spellbook. It’s usually much cheaper to pay the owner of a spellbook to copy just the spells you need (in addition to the scribing cost) than to buy the book outright.
Magic Items – I feel that magic items are too expensive when compared to mundane goods in D&D. A house sells for about 5000 gp and a +2 sword sells for 8000 (plus masterwork costs plus weapon costs). The sword is clearly a better value but I can’t think of anybody who would trade their house in exchange for that sword. Yes, I know that adventurers have different priorities, but still it’s not a good trade.
Favored classes – A favored class is only meaningful if you deviate from the class. A dwarven fighter gains no paticular bonus, while a dwarven cleric/fighter simply avoids a penalty.
Multiclassing in general – Mulitclassing is its own reward and its own penalty. There doesn’t need to be an additional xp cost. Unless you keep your two classess even. For some reason having a “double major” (cleric 5 / fighter 5) isn’t a problem, but if you take cleric 1 and then “change majors” to fighter 9, that one cleric level will always interfer with your fighter studies.
A couple of minor nitpicks:
Falling – In d20 you always land on your feet.
Running – In d20 running doesn’t make you go faster, it makes you go farther.
In response to some of the other topics brought up:
Reflex save – For some reason, they don’t bother me. I guess I am able to internalize that as part of playing a game.
Specialness of magic items – For the record, low plus magic weapons aren’t special. First, they are surprisingly common. Magic weapons are always near the top of an adventurers must have list. They have to be in world where monsters are trying to eat you on a dialy basis. Second, with the exception of penatrating DR of X/magic, you can’t tell the difference from a masterwork dagger (+1 enhancement bonus to hit) and +1 dagger (+1 enhancement bonus to hit and damage). Third, human beings have a minimum difference threshold of about 5%. So spotting a +2 dagger by it’s behavior in combat is going to be very unlikely even when compared to a non-magical masterwork dagger. Fourth, human beings* do* take things for granted. When was the last time you took the time to appreciate the rare and wondrous thing in your life?
Ninety-nine percent of the time people will look at that magic dagger and say “Yeah, it’s nice and shiny. What do you want to do for lunch?”