Were it not for First Contact establishing the idea that there was always a Borg queen, the fact that we suddenly see a queen after BOBW would have been a neat "adaptation".
After all, the Borg were defeated in BOBW because their one unified mind was tricked and reprogrammed. What better way to prevent that from happening again than having an independent mind overseeing the collective?
I find it hard to believe the queen was tricked into regenerating along with all the drones. Oh yeah, and then suggesting she used some interdimensional space-wedgie to get out or that she exists on a higher plane, come on. (Probably Braga's idea
Later on in Voyager, they come across a Human who was a liberated Borg. She said she was captured at Wolf 359. Um, what?