Chakotay, Tuvok, Paris could have been done better but it's also easy to way-overdo the conflict aspects with Chakotay and Paris. With the Maquis's conflict being about territory so far away it wouldn't make sense for there to be a huge amount of conflict on Voyager and OTOH if the conflict was about something more central to the Federation overall it wouldn't make sense for Janeway to make Chakotay first officer. Torres was done almost as well as she could be, despite occasionally being a bit static or inconsistent, while Kim, Neelix, Kes don't seem like particularly strong characters in general.
Some ideas for improvement in a new version.
Either have Torres be our main engineering character but not the chief engineer or have her be chief engineer but also have a Starfleet engineer like Carey or Taurik/Vorik appear much more often.
Make Neelix more of an actual expert and a diplomat (and security adviser) rather than a cook. Kes could also be more involved in diplomacy. Make Paris more low-position at least initially, like Ensign and on the security staff or transporter operator, rather than pilot, let Kim (also Ensign) or Chakotay be the pilot.
Ensemble. Sometimes the balance is off and it just doesn't work even with strong characters, and sometimes the Ensemble is greater than the sum of it's parts, even with weak characters.
I think the only problem with Voyager was the balance and interaction of the ensemble. I'm not a multi-million dollar a year Hollywood writer and producer, so I don't know how to fix it... but from my armchair certain things stand out.
Here are my opinions on the matter:
Firstly, the actor who played Neelix was not up to the role. He had the
look, but his acting skills did not do justice to the
part. I've said this here before, my apologies for repeating myself. Neelix could have been... no make that
needed to be so much more. His place in the ensemble was important... he was a comic "foil" for Tuvok and Paris, but none of it worked. The part of Phlox on Enterprise was similar. but Phlox was far more interesting, far more likable, and far better acted. And Phlox didn't have seven seasons to flesh himself out.
Secondly, the Torres character wasn't that good. Her duality comes off as pathetic, her "Klingonness" comes off as pathetic, and a few episodes just cement that. The character wasn't likable. Maybe she was supposed to be the ensembles "duality" character, but where Spock/Data/Worf worked, Torres duality didn't. It just made her unlikable. She hated her human side, she hated her Klingon side, she hated herself, and she was just angry. Worf was comedically gruff, Torres was just angry and hostile. And, when she wasn't... well you still didn't like her.
Thirdly, Kes. Everything that needs to be said about Kes has already been said.
Fourthly, Seven of Nine. Because the other aliens in the ensemble were so flat, Voyager needed Seven from season 1. She was the Spock/Data/Worf "internal conflict" character struggling with duality, trying to become "better" in some way.
The doctor can be considered an "alien" because of his situation as a hologram and as an artificial intelligence. His character worked, but unfortunately he had no background from which to draw interesting stories and storylines, andt least on a consistent basis.
Now, you might notice I didn't say anything about the human characters. That's because all the human characters in these shows are all the same. How interesting is Wil Riker? He's not, very. They're human, with human backgrounds. No matter how good they are, they are supporting characters for the alien crew. If you think about it, that's true of TOS, and TNG. TOS would have been very different without Spock, TNG would have been totally different without Data. Every one of these shows, even DS9 had strong alien characters in the ensemble for the human character to interact with.
Voyager didn't. Janeway, Chakotay, Paris, and Kim were all human.Their interaction with each other isn't all that interesting show after show. Until Seven, there really was no interesting aliens in the ensemble to drive complex story lines and complex scenes. But by the time she got there, the damage was already done.
I am glad they didn't use Paris' past and the Marquis' conflict to drive stories, though. That would have made it worse.