I just recently dinged 60 and did so mostly through questing (Horde side). Here are the quests that jumped out at me as really terrible for a variety fo reasons
1. Helcular's Rod - Hillsbrad
The first part of this quest involves getting the rod to drop off a Yeti in a cave. The problem is this has to be one of the lowest drop rates in the game. I killed like 100+ yeti for an hour before it dropped. Everyone else was int he cave killing too. Crazy low drop rate and the quest log doesn't even warn you about it, like it does some other low drop rate quests.
The final part of the quest involves putting the rod on a grave in a town surrounded by guards. At this point in the game the guards essentially kill you in 2-3 hits. It's just about impossible to sneak in and do it clean. You either have to corpse hop or have someone else sacrifice themselves to draw the guards away.
2. Powerstones - Uldaman / Fetishes - Sunken Temple
Same type of quest, collect drops off elite trash mobs. Only problem is the drop rate is extremely poor and you get very few of them INSIDE the dungeons. You mostly get them off trash elites before the dungeon. These are the mobs most people try to skip anyway, getting a group to farm them is very difficult.
3. Linken - Ungoro
The Link (ala Zelda) inspired quest from UnGoro has some of the worst pointless travel involved. They make you go from UnGoro to Winterspring and back about 3-4 times.
4. Killing Moonbeasts - Felwood/Winterspring
Ok so an NPC in Felwood wants you to kill Moonbeasts in Winterspring, very inconvenient for the quest giver to not be in the zone you're expected to do the killings. Well the kicker is he keeps sending you back over and over again, to kill specific TYPES of moonbeasts. And you get to the moonbeast camp and there are 3-4 types there, so inevitably you kill lots of hte wrong type, well then he sends you back to kill a different type, it's just ridiculously pointless.
5. Seal of Ascenion - LBRS
I don't mind attunements, they actually make sense to me. You gotta prove yourself on content X before you are worthy for content Y. That's typically how most attunements in the game work in theory. Wanna go to MC? Ok you gotta do BRD at least once.
Wanna get the UBRS key? Ok well you gotta do LBRS first. In theory the quest should involve a single full clear of LBRS but the way it's designed with the gem drop rates, the average player who is just pugging will have to run LBRS fully on average about 15 times before they get their seal fully complete.