I think BGBuddy is important, one because its a nice leveling alternative, and two because a lot of people use it get their ilvl up to heroics point. It's no secret how full of botters BG's are currently, having the bot a bit smarter to ninja cap flags, move to logical points and not "biggest fight" would be very beneficial.
Gatherbuddy2 could use a little bit of help, it works well enough, but has a lot of trouble with landings, trees, buildings, ect. A stuck helper there would be brilliant.
Questing, I understand is being worked on again, but still is littered with issues (granted many are being reported and fixed up)
Pet battles... interesting, but I'd put them low in que.
Honestly, the main thing I would really love to be improved is Dungeon buddy. It's a brilliant idea, great leveling, and gets nice gear. I have a 5-man team I run (usually with me as tank) and lately I can't even use it. Constant stops, not moving, and the bots are extremely hesitant to attack. Not to mention they have great trouble navigating certain instances like Wailing Caverns, All the Blackrocks, and such. Mists support would be beautiful, and the few dungeons that are heroics only. I don't expect my bot to be perfect, but moving out of bad stuff and jumping to avoid firewalls and such is kind of obvious to not looking like a bot (or getting kicked for being partially retarded.)
I think a lot of what people want is for their bot to do it's job without constant supervision. (And fear... paranoia is rampant with BGBuddy right now)