Okay, I've finished re-watching Voyager, and I am ready to confirm it was the worst in the franchise (shocking, I know). I was going to do a top 5 worst characters, but that seemed to easy, so I' passed up the low-hanging fruit and and went with the top 5 best Voyager characters. Let the debate begin!
http://kooztop5.blogspot.com/2012/03/top-5-best-star-trek-voyager-characters.html
I have to say that I completely disagree with your assessment of both VOY and Janeway. Was VOY a great show? No, but neither was TNG, DS9 or
Trek in general. They have their moments, but none of them are as good as the best television shows out there. And I think it is pointless to compare one franchise to the other, because, really, how different are they? How is DS9 better than VOY, or TNG better than DS9? They all have underdeveloped characters, weak dialogue, missed opportunities, etc. Yes, maybe DS9 had more continuity, or TNG occasionally dealt with weightier issues, but VOY had its highlights too and calling it "the worst franchise" is just being nitpicky. The different shows just aren't all that different from each other and none of them are that great (though they are entertaining and I'm a fan of them all!

)
As for Janeway, what can I say? She's awesome. I know a lot of people don't like her, and of course everyone's entitled to an opinion. But I just disagree with the haters. To those who criticize her actions, I would say, she has balls (so to speak), she takes risks and gets things done. To those who criticize her inconsistent behavior, I would say, what do you expect? This is
Star Trek and sometimes the writing isn't great. Sometimes characters make U-turns (see Jadzia Dax), although really, I never found her behavior all that inconsistent.
Now that I got that off my chest, here are my lists:
Best VOY characters:
Seven - Well-developed character with interesting storylines.
Janeway - See my comments on Janeway above.
Tuvok - Cool and competent, sometimes seems to be the only "adult" on the ship. Could have been developed more.
Torres - Had some good storylines; I especially liked her mother-daughter relationship with Janeway in "Barge of the Dead."
The Doctor - Could be extremely annoying, but he was one of the more developed characters.
Worst:
Kim and Paris - Bad actors and whiny, irritating, immature characters.
Chakotay - Not great acting and unfortunately kind of left to the side by the writers.