I feel like this thread asks two different questions - Who is my favorite, would be the one I enjoyed watching most, which is proabably the Doctor simply because I enjoyed his performance immensely.
The BEST Voyager character (IMO) would be the one with the clearest character arc and growth realized through the series, which of the main cast I think is Paris. I think they wrote for him well, and wrote a character that hadn't been realized on Star Trek before. Obviously based on Lacarno, I see him as being what Ensign Ro should have been had she not suddenly joined the Maquis at the end.
Seven, Torres, and the Doctor I felt were somewhat stagnant. Seven attained a certain level of borg-like humanity and then just permanently stopped development. I'd have liked to see her break from the computer-like surly cadence of her voice into something more natural, for example, as time went on.
Torres was over and over again dealing with her supposedly volatile Klingon half and/or heritage.
Doctor at his core was Data 2.0, but as I said, I think Bob Picardo did a fabulous job with it. I actually enjoy watching him more than Spiner at this point.
Kim, Tuvok and Chakotay really suffered from the same problem - their characters weren't allowed to develop from where they started. It was particularly bad for Kim, because he was never allowed to consistently express any sort of confident, seasoned version of himself even 7 years later. Yeah, there were episodes like Nightingale, but he didn't seem to carry those sort of experiences with him later.
Neelix? I'm not even sure what the point of Neelix's character was supposed to be after he split with Kes. He wasn't particularly wise or insightful. He didn't hold a mirror up to humanity and make us think about ourselves. He cooked leola root, organized social functions, and pretended to be an ambassador (I guess so he could feel important). Not that they needed an ambassador - Janeway was always the one mediating disputes.
Speaking of Janeway, I like Mulgrew's performance, and I liked the character, but when one starts out knowing nearly everything about everything, where is there to go? Now I understand Q's fascination with her! She's already part Q!