I think even the writers/producers/studio heads realized they were churning out half written, lazy garbage. The season reached a despicable low point with "Favorite Son" before the quality of the writing spiked dramatically starting with "Before and After" although that isn't to say there weren't good episodes before those last few of season 3. "Unity" was actually pretty great.
Also wasn't it weird how VOY season 3 somehow feels more old-fashioned than season 1 and 2? I think it was something to do with all the rubbish that seemed like they were from TNG reject scripts (Warlord, Favorite Son, Rise etc).