I'd say...
1) No matter the background chosen concerrning Chakotay aka his origins (coming from an native american tribue) or his psychology (half proud warrior and/or with an unusual wisdom), they (= producers/writers), should have stuck to it from beginning to end and not change suddenly because they did not know how and what to do with it.
(I don't think that the firing of expert in Native American culture hired by the production to advice and prepare Robert Beltan*, was the only reason of the outright abandonment).
(* it seems that Beltran has done no research on his side to try to understand his character -> by lack of interest or sheer laziness, I don't know !)
2) no romance or attempt to romance with the Captain Janeway* or Seven, except a deep respect and loyality (Janeway) and a real understanding & acceptance (Seven).
For a soul-mate and not just a love interest (as seeing as Siska was killed off and Kellin, just a one night stand), Lt Marla Gilmore would have fit perfectly (a Maquis rebel leader with a Equinox's pariah).
-> *if Janeway is married to Starfleet and Seven still in search of her humanity, Chakotay
may well find love with someone smart & lovely who really love him in return.
3) no Starfleet uniform for him and his team ->
You can't judge a book by its cover.
-> if Chakotay is a Maquis rebel, that he dresses and behaves as such. At least, there will be no margin of error when it will come to his decisions.