Well the problem with Chakotay not differentiating himself from Janeway is a microcosm of the whole dynamic of the Maquis and Starfleet crew members. They were too similar. Hell, most of the former Maquis were former Starfleet officers, who were drummed out or left on their own for one reason or another. Well, except for Seska.
But other than a few episodes of grumbling, how were the Maquis really all that different from the star fleet crew? They had similar principles, wore the same uniform, and with Cardassia on the other side of the galaxy, the main reason for their conflict was rendered irrelevant.
Now, with Chakotay in particular, he had a lot of potential, but it was wasted. First off, he was from some unnamed generic native American tribe. They should have made him of a real tribe with real traditions. Instead, we got a mish mash of all kinds of tribes. When they made his tribe descended from aliens, it just cheapened his Native American heritage that much more.
Second, I also agree he should have been more like a toned down Edington, and Janeway and Chakotay should have had a history of being enemies prior to being stranded. Sort of like maybe Chakotay and Janeway served together, and Chakotay somehow betrayed Janeway, or tricked her somehow, when he joined the Maquis. That would have been more interesting where you essentially have two captains who don't get along, but are forced to work together, but we didn't have that very long. Chakotay became very friendly and loyal to Janeway very early on...maybe a little too soon. It would have been nice to see two people who hate each other gradually respect each other, and then become friends, and maybe even lovers at the very end.
Which leads to another thing, the Seven\Chakotay thing was straight out of nowhere, and ruined chakotay's character, to me.