Well, with Chakotay the problem also was that Beltran was phoning it in nearly from day one.
The Maquis, in general, were just not fleshed out enough to really work as the Foil to the Feds they were meant to be. Either the "other group" should've been a bunch of DQ aliens who were also on the Array when it blew up, or Romulans (since Cardassians were already getting plenty of development in DS9).
Self-loathing half-klingon. Well, I guess that's a personal thing because I never thought that was interesting.
Kes, yeah there was room there. They should have expanded on the Ocampan lifecycle better: She should have been introduced as a kid, be a teenager by season 2-3 (a young one in S2, a mature one by S3) and a mid-20s adult by S4.
Neelix as well, I don't see why they didn't use that good backstory more.