Voyager went wrong the moment the Maquis put on Starfleet uniforms. (In fact I found it sort of ridiculous even the Starfleet crew were still wearing uniforms after the second season or so).
A ship stranded alone in the Delta Quadrant should have relied on internal conflict to drive plot, rather than bland aliens-of-the-week, or worse, spatial-anomalies-of-the-week.
There did not need to be open hostility between Starfleet and the Maquis, but some acknowledgement in the character development that they were different kinds of people from different backgrounds.
The ship also had a fairly small crew complement, so there was no reason we couldn't have got to know everyone. I think the show would have been truly great if they had developed serialized concurrent plot threads in different parts of the ship, and made it a true ensemble cast.
Instead, we got the Janeway/Seven/The Doctor hour, where you get a brand new ship every week, and all your problems can be solved at the end of the episode by reconfiguring the deflector dish.