I never really had that much of a problem with Chakotay. But he seemed too calm and at peace, and agreeable to with Janeway and Starfleet in general, to have been a Masquis. I think they should have written Chakotay to but heads with Janeway more, at least in the beginning, sort of the same way as B'elanna, and showed him change and become more at peace with Starfleet, and maybe himself. Also, I think they should have, instead of writing him to be from a generic, made up Native American tribe influenced by Delta Quadrant aliens, they should have made him from a real tribe (IE Navajo, Apache, Hopi especially, since he was supposed to be from the US Southwest~or mixed tribe heritage). Instead of using stereotypes, they could have introduced REAL native culture to the audience.