I think it was bizarre from the start because, in order to have any real grasp on the Maquis, you needed to have regularly watched DS9. I don't think it was smart for the writers to have assumed this. I saw most of VOY before I ever managed to watch DS9 (mostly because DS9 aired randomly on Saturday afternoons and was regularly pre-empted by sports), so throughout most of VOY's run, I had no idea who the hell the Maquis were even supposed to be. All VOY gives you is a little blurb at the very beginning of the show saying that they're criminals.
I finally managed to watch DS9 straight through on Netflix last year, which I immediately followed up with a VOY rewatch, so I appreciated some of the continuity (ex: the episode where Chakotay and B'Elanna find out that the Maquis in the Alpha Quadrant have been wiped out). The thing about the Maquis, though, is that most of them are either former Starfleet officers or former Federation citizens anyway, so adapting to life in Starfleet again really shouldn't have been all that difficult. And with no Cardassians around, they shouldn't have anybody to really be pissed at.