I've always wished the Val Jean had not been destroyed. It would have made for an interesting dynamic but with the first female captain it was all or nothing. A shame but it was the 90's.
That would have added some interesting opportunities for sure ; based on the reg's from Exquinox , Janeway would still have authority .... except if the Maquis ship was still around would Chakotay have been so willing to follow star fleet regs ?
I think they could make it work since his ship was inferior to Voyager. A quick line about how that class of star ship is designed to have a full overhaul every 10 years, no chance of it lasting all the way to the alpha quadrant without support form a mother ship. I think the show did a good job of showcasing Voyager as a state of the art star fleet vessel, and they still ran low on power and such.
They could still use the lost of life during the arrival as a reason to intermix the crews. Maybe B'Ellana is the only one left alive who knows how to manage the type of warp core on Voyager, but then a junior engineer from Voyager needs to go and help on the Val Jean since they need someone to engineer.
Does anyone know if the Star Trek comics ever do a 'what if' series like Marvel does ? this could be a neat idea