1st edition: level limits, distinct and non combatable mechanics to be stealthy (and surprised) or listed at a door, the need to give treasure for advancement (XP) and then drain it away with training, weapon speeds, a weapon vs. armor chart in the PHB that no one used, a bunch of weapons no one used, psionics, much of Unearthed Arcana in play (for some reason, I liked it better in Dragon), much of the Fiend Folio (this was probably my first realization that game designers where not perfect, but now it does have a certain nostalgia value)… as an aside, other quirks I kinda liked: spells balanced with system shock checks, disappearing drow equipement…
2nd edition: keeping too many of the above, but without the charm or style. Two weapon rangers, most kits, most things Realms that I had contact with, the devastating long spear from the CFHB, the complete elves handbook (and all released after it), large portions of Players Options in play, including sub-ability scores…
3rd edition: the 3.0 ranger, 3.5 weapon sizes (given what they replaced), too much emphasis on a default setting (including things like deities, demographics, magic level…) that can never satisfy everyone, no matter how generic they make it.