There are a lot of things that would have made VOY better. I definitely agree that UPN's intereference played an important role in the direction the series took.
It would have been nice to see the original premise remain in-tact: one little ship all alone, in uncharted territory, with two conflicting crews who are forced to work together for survival. I didn't want to see the Starfleet and Maquis crews working side-by-side, happy as can be, like a big, happy family. Keep the Maquis out of uniform for a good, long while. Maybe even keep some of them in the brig? Have Janeway torn about whether or not to integrate them into the crew, what sort of ranks and jobs and authority they can have, etc. I'd have a LOT of tension between the two crews - more than what we got in the first half of season 1, and it would last a good, long while. Maybe some of the Maquis would consider over-taking the ship, or they'd want to leave Voyager and go off on their own to find a way home?
The character development needed work. I'd like to see more consistently-written characters, with more interesting stories. And please give them something to do! The final seasons really focused on Janeway/Seven/Doctor with a few B'elanna stories thrown in. Harry and Chakotay were seriously under-developed. Every Tuvok story seemed to involve him going crazy. I'd toss the Neelix character out the window, or maybe have him recurring instead of a series regular. Kes was a missed opportunity - I'd have kept her aboard and given her something more interesting to do. The concept of the Ocampan life cycle (live for 7 years and die) could have provided for great story potential near the end of the series.
Continuity would have been nice. More story arcs, more recurring characters and on-going plot threads. Let battle damage from previous episodes carry through to other episodes. As many people have already stated, Voyager was too clean and tidy. There's limited resources out there, and no starbase for the ship to dock at for repairs, so how the hell did everything stay so shiny and new?! I want to see the crew desperate for help because systems are failing, resources are depleted and they don't know what to do. This show should have been about SURVIVAL but this crew had it way too easy.
People love to compare VOY to BSG, and I have to agree that BSG does it all better. Part of what drives me crazy about VOY (and a lot of Trek, in general) is that despite the circumstances, everything feels too safe. It doesn't matter that the ship is out-gunned and all alone and characters' lives are in peril - in Trek, everything always turned out A-Okay. And that gets really boring.