My theory with "Counterpoint" is that Janeway was manipulating Kashyk the whole time, and she used some seduction to do it. Come on, who can't see that Kashyk had the hots for her
as well? There was sexual tension between the both of them in that episode.
Janeway and Chakotayhad tension from early on, but I think it made sense for them to not get together on the show (as much as I would have liked them to). But like Nightdiamond
said, it would have been nice to have seen them actually kiss and acknowledge that attraction, but realize that they couldn't have a relationship because of duty. To me that would have made much more sense than the dancing they did around the topic for seven years.