She wasn't too bad in First Contact. The movie implied that she was simply an avatar for the Collective, not too different from Locutus. Later writers didn't get that and VOY turned her into an individual within the Collective who controlled all of it, somehow. Then her depiction just kept getting further and further from her depiction in First Contact, mostly keeping superficial things.
Section 31 went through a very similar shift, where DS9 implies that Sloan and S31 are rogue agents and Sloan is talking out of his ass in regards to any real authority and taking an, at best, extremely liberal interpretation of the Starfleet Charter, then later works making them an official part of Starfleet.
I don't think that's too big of a concern, to be honest. You can't negotiate with a spacial rift and the show handles that kind of thing fine. I think they were having problems with First Contact's script and decided to solve it with a named antagonist rather than just hordes of Borg.