The only thing I'd really call different compared to other MMOs I've played is the more action-y feel of combat rather than just simple math functions going off automatically or with a button press. Some might argue Tera did it first, but I think GW2 took it a step higher. Meanwhile, Rift did meta-events to basically comparable quality and ingenuity. Honestly, they're just randomly triggered quests. So I can't quite say they're innovative there, and Rift is also looking to up the bar on their events come their November expansion release. The rest of the game mechanics are pretty standard fare, maybe even a bit too much on the mundane side. The prevalence of bugs also isn't help Anet's credibility, F2P or no.
I won't speak on PvP much because it generally disinterests me. I can also point out three glaring reasons why. First, queues. **** that. Second, the general futility of being an individual player. Some may revel in the power and concept of collective zerging, but you're just not going to be organizing random people well enough to adopt actual strategies. Third, off-hours capping. Did you work hard to capture and upgrade that keep? Too bad, some people in a different time zone are gonna undo your work while you and everyone else sleeps.
Two and Three are points I've had contention with when playing Aion back in the day, though with a slightly different spin on the third point. Zerging prevailed there, too. Didn't help when you had a bunch of PvP twinks headbutting with a bunch of PvE casuals, either. But the real issue I'd disliked about their fort system was restricted windows of access. This is sort of the inverse of GW2's problem, where you could've had all the people in the world ready and willing, but you simply couldn't conquer a fort because the game wouldn't let you.
I'm honestly not sure what Anet could do about it other than making it easier for smaller groups of people to invade whenever, but some might argue it'd make it even easier for night crews. On the other hand, keeping a fort when you can defend it usually isn't too tough. So the only defense is to have your own night crew at present. Either way, blah at it all, and add a fourth gripe in WvW repair costs on death.
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Violence good. Sexy bad. Yay America.