Voyager should have made Year of Hell a season long arc. The way the Equinox was when they found that is a much more realistic notion of what should have happened to voyager over the years as well getting steadily damaged and making hard choices and morally amiguous decisions.
Guess it was all under the curse of syndicated television, can never have any major changes to the status quo that would confuse the casual audiance.
The whole Marquis storyline was always so watered down, there was potential for some really good conflict between the 2 crews that was never properly explored... closest I thought to being like that was Worst Case Scenario and that was a flippin holodeck episode.
I don't think the Borg got overused, they just became kittens and practically got bullied by Voyager, when Janeway, Tores and Tuvok got assimilated in Unimatrix Zero I remember being so annoyed as it was so 'all in a days work', basically it secured the Borgs transition from scariest strongest threat to the Federation to being on the same level as the Cardassians and Klingons.