Watching VOY i have to wonder. How did Chakotay ever reach the the rank of LT. Commander in Starfleet? While the details are hazy. StarTrek.com and Memory Alpha both hint that Chakotay was a Lt. Commander when he resigned his commission. When you watch the TNG episode "Tapestry", Cmdr. Riker says you have to stand out and get noticed in order to be promoted. Hell even Troi was Lt. Commander in "Encounter at Farpoint".
Chakotay doesn't do any of thing to stand out on VOY. He doesn't have any command presence either. Events come along once in a blue moon like "Scorpion". I just don't see how Chakotay could've climbed the ranks to Lt. Cmdr. His Cmdr rank is a provisional rank instilled by Capt Janeway under extreme circumstances due to Caretaker. He's just so bland and uninspiring it seems implausible.
I see no reason not to see why Chakotay couldn't have risen to Commander and/or higher. He was a quiet, soft-spoken type but he was apparently very effective as a guerilla warrior against the Cardassians.