Chakotay, like a lot in VOY, never really hit his mark.
He was supposed to be a fearless and bad-ass terrorist leader/freedom fighter, but after he puts on the uniform he just becomes Janeway's whipping boy. The will they/won't they dynamic they had in the first couple of seasons fizzled out to nothing.
As other have said he was had some pretty stereotypical aspects of his heritage shoehorned in unnecessarily, but nothing was every really developed further.
In a situation where they face uncertainty with every day, you need an XO who is dynamic and daring, someone who will follow the Captain's orders in public but will argue with them behind closed doors. Janeway should have been portrayed as a more "cautious" Captain, with Chakotay willing and able to fly off the handle at a moments notice--his time with the Maquis should have made him a little reckless.
As for the whole Chakotay/Seven thing, that came out of nowhere, went nowhere and did nothing for anyone--except leave fans scratching their heads and wonder WTF was that all about?