The skill queue. For some, the fact that learning skills are time-based is an absolute turn-off to playing Eve Online. For me, creating and maintaining my skill queues is an interesting mini-game that I spent most of my dedicated Eve time on this weekend.
Grasping and accepting the skill queue in Eve takes a different mindset than when playing a fantasy MMORPG like World of Warcraft. In a fantasy setting, a character learns skills through actually performing actions. In the world of New Eden some 210 centuries in the future, learning for capsuleers is performed by implanting the skills into pilots' heads. So for pilots, the skill queue is an important part of life. If this sounds like I'm a role player, well, the "RP" in MMORPG does stand for "role playing".
From a design standpoint, I think the current skill system makes sense. One, Eve has a big enough problem with macro'ers without giving another reason for players to do so. See Darkfall for an example of a PvP game that winds up with players macro'ing to develop skills. Making the gaining of skills time-based takes away that incentive.
The most important aspect I like is that the skills leads players to create their own "classes". Perhaps more importantly, the players then behave like those capsuleers actually should. Let me use mercenaries as an example. Alekseyev Karrde, the founder of the Noir. Mercenary Group, is one of the top, if not the top, mercenary commanders in Eve. He runs his corporation as a professional organization and his pilots act that way or they are out. In contrast, there is no such penalty for a paladin in a game like EverQuest 2 from acting very unpaladin-like. Perhaps my background in pen & paper D&D influences my opinion, but a player's actions should have consequences. In Eve, they do.
I realize that I have slid away from the skill queue and into how players choose to play. But in Eve, player social interactions are also another way to develop characters. A pilot is not just a set of statistics. A character is also judged by their status with NPC corporations and factions, the contents of their wallet and the corporation and alliance they fly with. Moving up the ranks in a corporation is every bit as important, if not more important, than the skills a player possesses. Skills count, but so does interaction with others. A lot of players forget that and just concentrate on stats. The really successful ones don't.