Unfortunately, we can't help that some developers are just plain lazy, and don't want to update their stuff to work with the new API changes. We've been working very hard to keep most things backwards-compatible, and have. We had to reorganize quite a few things, because they were simply out of place, or didn't belong somewhere. (Eg; why was QuestFrame in the "Inventory" namespace. Stuff like that made no sense) We figured with the new xpac, was the best time to do a mass cleanup so we (hopefully) won't have to touch it again.
As far as questing goes, QuestBot does work fine 99.9% of the time. Some quests do require some extra attention now, due to Blizzard changing how things worked (this is why we originally added the ability to "override" a quest objective, in the off-chance that the bot doesn't get it right by using what WoW gives us). Unfortunately, Kick is moving house, so he's not around to update his profiles.
AutoEquip will be getting fixed either today, or tomorrow. I need to go through and update all the inventory slot stuff, for the new changes. (No more relics, thrown weapons, etc)