I'd love to see more in depth and interesting quests in this game, and I think we will, but that sort of content is extremely polished and I don't think FFXIV is quite ready for that type of development sadly.
Also, while a lot of WoW quests are bland kill X for X drops, I felt Cataclysm introduced some extremely interesting quests (especially within Ulduum, the whole Indiana Jones arc of quests). I mean at one point I was gunning out the back of a plane... that was some original shit for WoW and it really excited me.
With that thought, I would like to see this game branch off the beaten path as well. You mentioned the Pugalist quest as interesting, though I personally sort of felt like it was one in the same with most other quests aside from maybe picking up the money knocked all over (but WoW has plenty of 'pick up intractable item on ground' quests).
So the real question is, WHAT makes a quest "unique" these days and interesting? While dreaming is fun, one has to also be realistic on what the game's engine is capable of... and in those constraints, what could SE provide us that would satisfy?
I certainly don't think "Kill X of this monster" or "Kill this monster for X of a drop" cut it, though they are bits that can sometimes be utilized and not be so bad... I mean it's a fantasy game, we're going to kill things. So, at some point, "Kill this mob or X of this mob" is going to pop up, and that's fine if it's interesting or a challenge.
But when you look at SE's talk of monsters with multiple targetable limbs, etc, we enter the possibility of "Go find monster X, which is far too strong for you to defeat, lure it to this cliff and knock it off balance and over the side." Is that a bit more interesting? I would certainly think such a thing possible, especially in 2.0. Truth be told, I think more interaction with the actual environment is required, especially in fights.