Although it's not my favorite Trek series (I don't often have a hankering to rewatch episodes the way I do with even Enterprise), I think Voyager gets unfairly maligned as TOS part 3. It's a little too easy to point to single episodes and say, "that's why Voyager was so bad," as if the other series didn't have their crewmembers transforms in strange ways. I do think the show went too many times to the well with the Borg, diluting one of the franchise's more powerful storytelling tools.
On the other hand, I think that the first two seasons are more assured than the other series. Although the Kazon could seem to be derivative and unbelievable in their incompetence, they were certainly the right size for villains for the ship. Indeed, if the story had remained in the Alpha Quadrant, Janeway et al would not be taking on the same tasks as Picard. It's missions would be smaller in scale, and the villains would need to be downsized appropriately (unless, of couse, the ship became involved in the Dominion War).
Of all the little things that could have been done to improve the show (like not focusing on three characters and pissing off the rest of the cast), there's really only one thing I think would have drastically improved the show: that Mulgrew was invested in Janeway the same way Brooks was invested in Sisko, putting forth not just a de facto vision of a women in charge, but making the character a focus of commentary on femininity and authority. (I'm sure people will disagree with the assessment.)
BTW, I didn't vote in the poll--too simple.