I personally disliked a lot about Cata. First, the questing on rails. Don't like this quest? Too bad, you have to do it anyway or you can't go on to the next quest hub! ...on every alt! The number of times I missed the dungeon queue on my dps characters while questing in Uldum and being stuck in some video I couldn't cancel... the rage.
I still have no clue why we killed the bosses in BWD. There's no quests (at least not at Cata level - I never redid the lowbie quests as I had already done loremaster and I'm no great lover of questing) pointing there. Almost the same with BoT. Cho'gall - sure, but all the other bosses? Saw Valiona before, but no idea how she's involved with the plot other than showing up in BoT and Grim Batol. And Al'Akir, why did we kill him?
Firelands as a raid was okay (if a bit small for being the only raid that tier), especially Raggy, but it just didn't feel like a living instance to me. What was Rhyolith lord over and why was he stuck on that island? Same with Beth'tilac as she was just sitting there in her spiderweb not doing much at all. We were supposed to attack Firelands because they were going to invade Mount Hyjal, right? But that's not what I saw at all in there. They just seemed to stand around and chill, no preparations for war anywhere. Compare this with Karazhan where the ghosts actually seem to live regardless of whether you are there or not. Or Mount Hyjal where the mobs actually came to you, attacking where they feel like rather than waiting for you to walk up, discuss tactics for a bit and then attack them.
It's a bit similar with Dragon Soul. Once again too small, once again I'm not sure why we killed some of the bosses in there. Sure, Mor'chok was in our way so I get killing him, but Yor'sahj and Zon'ozz? I mean we even had to take a flight path to get to them and they didn't really seem to hold anything important like Hagara. The mechanics of Spine felt really meh as dps and heroic Madness wasn't that great either having to stop dps to wait for tank cooldowns.
While in MoP, I can actually understand why we're killing the raid bosses as they're connected to the quests outside, to the lore in general. I just hope the future tiers will have a decent amount of bosses anchored in the in game lore as well.
Actually, the one thing that I really don't like in this expansion (apart from too many dailies) is being teleported in somewhere random in the instance after running in after a wipe. It's really annoying on progress when you want to go back out for a repair. Though I imagine it's even more annoying for 10mans entirely without engineers or warlocks.