Kes was an ill conceived character to begin with. And simply making her Neelix's possession did even less to help develop her character. I think the show tried to have too many characters in the ensemble. I know some people like her, but what really did the character add to the show? She simply forced tension between Neelix and Paris. Not having her would have allowed more screen time to develop Paris or Harry more.
I think having her on board contributed more to the soul and "feel" of the early Voyager years than Harry. What did he really add in that time, except for being the token newbie who still wants to do everything by the book and missing his family and Libby?
What did she add to the show? I think her character wanting to experience everything in her short life and explore the universe was the epitome the Star Trek ideal.
Ensembles are like... albums. Sometimes, an album will be far greater than the sum of it's parts, because the parts work and flow so well together. Sometimes the opposite is true; an album of equally good songs just doesn't work. It's an odd phenomenon. A lot of the early "Eagles" singles didn't crack the top 20, but put them all on "Their Greatest Hits" album, and for some reason it becomes the best selling album in US history, still selling to this day.
The Voyager crew is like an album where a few misplaced or underdeveloped "songs" weaken it too much.
My opinions:
Best characters:
Janeway: Best captain, since the original James T. Kirk. 'Nuff said.
Chakotay: I think the character would have worked better in a better ensemble. That is, I think Chakotay was a good character, too many of the other characters weren't. He did well as the main character in several stories, and he was an important supporting character.
The Doctor: Standout character, capable of carrying complex story lines, as well as an important supporting character.
Seven: Another standout character that carried many complex story lines, as well as an important supporting character.
Tuvok: Tim Russ knocked Spock off the throne as my favorite ST character in general. I wish there was a few more Tuvok-centric episodes. Well acted and interesting, did well as the main character, and was an important supporting character. What I consider to be a "real Vulcan"
Here's where the problems start:
Harry Kim: The young Ensign Kim angle got old
really fast, and there was nothing else to the character beyond this. They were going to knock him off but didn't. I consider Harry a pivot character. If he was a better character, there would have been far more balance in the bridge ensemble. He was not a consistently interesting character.
Tom Paris: I like the Tom Paris character, but like Harry Kim, they never took the character anywhere. I think if the Harry Kim character was better, Tom would have worked better. He was not a consistently interesting supporting character, or lead character. I really want to put this character in the top list, but I have to be honest.
Neelix: Someone wrote that "Phlox", the doctor on Enterprise was what the "Neelix character should have been". I think I understand this. Phlox was a strong, well acted character, where Neelix really wasn't. The character of Neelix had so much potential, but in my opinion Ethan Philips can't act (from what I've seen in Neelix, and his other TV appearances over the years), and so that potential went untapped. The character was needed to be a strong supporting character, but just fell flat. What was wrong with Neelix? Ethan Philips.
Kes: Kes was portrayed by a much better actor than Neelix, but there really was nowhere for the character to go. There was some initial interest with the character early on, but it quickly became obvious that she wasn't adding very much to the show (sorry Kes guy!) Maybe if some of the other characters were stronger it would have worked, but... , She did not do well when she was the story lead, but worked well as a minor supporting character.
B'Elana: Angry Half-Klingon Ho hum. They should have killed off her human side when she was split by the Vidians. Imagine that. That woud have added some juice to the character. Was an inconsistently interesting supporting character.
Just my thoughts. But, I think the DS9 ensemble was worse.