Early Voyager made Janeway/Chakotay possible but they seem to kill it after 2 seasons. Was there ever a explanation by B&B why they dumped it ?
Likely it was dropped for realism in a command structure. Relationships with subordinates even in extraordinary circumstances is typically frowned upon.
In terms of the best 'couple,' in the Voyager series I really shocked that Paris and Torres didn't win this hands down. It was the most realistic and the actors did an excellent job of portraying realism in tension that often exists between a couple in real life.