My personal quirks primarily focus on the weapons chart. Several weapons seem to serve no real purpose, and while I understand that some weapons were actually better than others, the worse weapons were normally cheaper. The trident being a more expensive, harder to use spear bugs the crap out of me!
My other irritation is the metric monetary system. 3E decided that it was too hard for people to do math, so they dumbed down the currency. In AD&D the metal coins were based (estimated) on the historic value comparison by weight, which gave us 10 cp per sp, and 20 sp per gp. I don't know if electrum and platinum were accurate, but it worked well enough. I could accept it if it were presented as based on purity and coin size, but in the trade goods section a gold bar is exactly the value of its cost in gp, indicating that coins are "pure."
The idea that nearly everyone can read and write.
...I should probably stop now.
This bugs me a bit too, but it's been around a long time. The problem is that unlike other games, D&D is designed to be generic fantasy, and they simply can't assume the literacy rate of a setting. Thule added a nice option for determining literacy which I've incorporated into my Greyhawk campaign.
Related to that... I'm not a fan of the 5-foot square as the baseline measuring system.
I feel as though it leads to weird dimensions for buildings, doors, and a variety of other things.
I would vastly prefer that a 1-yard (3 feet) square be used. In metric, that would be roughly 1 meter per square.
The 10 ft passage was a staple of the original game, as they used 10 ft (or 100 ft outdoors) as the standard grid size. However, spacing was much closer to 3 ft per human, as a front line typically consisted of 3 characters. I'm not certain, but I assume that's because that's what it was in miniature wargaming of the era. I do recall in 1E they had a required area to use certain weapons (e.g. a greatsword required at least 6 ft around you to swing properly) which impacted this. I think this is a far better system, as it also remove the "moving through other's space" situation, since you just can't do it.