Voyager had plenty of good bad guys of the week, and recurring bad guys didn't make a lot of sense anyway, aside from maybe the Borg, being as dominant as they were.
The Kazon were the most awful bad guys in Trek history, but they ditched them really quickly by the start of the 3rd season, and incidentally, the show instantly improved dramatically. Then it improved further once they got 7 of 9 and switched to full CG spaceships and battles. I think the show had a lot of the best action scenes in all of Trek because they were able to use CG.
Overall I think their one off aliens were as good as any of the other Trek series, as they had to rely more on them due to not being able to return to the familiar ones all too often. And when they did, they ended up being horribly contrived, like the random Klingon tribe, or the Ferengis who happened to get stranded along their path, or anything involving Troi and Barclay. I would have preferred they have no contact with Earth at all until the finale, then see the shock as they arrive, instead of the deflated ending we got.
Kind of a random tangent, but there was a funny line in the most recent episode of NTSF:SD:SUV. One of the main characters is played by Kate Mulgrew, aka. Captain Janeway. They were investigating an alien, and she says "Aliens don't exist. They were made up by Gene Roddenberry so indoor kids could have something to live for."