Seven and the Doctor were the obvious choice. They had been developing that one from the beginning. They were at similar stages in their emotional development and the Doctor clearly had romantic feelings for her.
Similarly, Chakotay and Janeway were being developed to be a couple for years but trek doesn't like captains in committed relationships. The episode where the 2 were facing being stranded alone in a planet showed the attraction plainly.
Seven was hot but had the emotional level of a teenager. I don't think the relationship made sense to anyone but I don't think it was Beltran's decision but a production one. Fortunately the books tried to refocus on Chakotay/Janeway but they seemed to have forgotten about Doctor/Seven.