The Voyager writer's room clearly had some
ideas for the characters in the beginning. But unlike TNG or DS9, where an ensemble dynamic ultimately prevailed, VOY simply developed in a way where a few breakout characters (the EMH in particular) clearly asserted themselves over time as being far more interesting to write for than the others.
Chakotay unfortunately just ended up being one of the ones whose character traits as described in the format document weren't enough to hang seven seasons of storylines on. And as others have said elsewhere, it certainly didn't help that the Maquis storyline, which let's face it was pretty much his whole rason detre for existing in the cast in the first place, was dropped almost immediately by order of the network. Having said that, they still found things for him to do..... but they simply weren't very interesting