The main problem with Chakotay was that he really wasn't all that different from Janeway in the first place. A principled leader type. They didn't try hard enough to differentiate them to begin with.
Also, they made him less of a traitor than most Maquis. He formally resigned and then joined, instead of defecting and selling out secrets, etc. This, again, sort of undercut his character.
Jeri Taylor never allowing Janeway to be in the wrong sure didn't help matters though.