One thing I got out of the Sullivan relationship is that we actually see what Janeway wants because she programs him. I think its very significant that she says "make him more provocative". Chakotay is really lacking that, it's not a word you'd ever use to describe him. Perhaps if he had been less passive Janeway would have found her resolve to put her Captaincy first a little more challenged.
I rather liked Jaffen. I don't think she was in love with Kashyk at all but she was quite likely in lust/attracted to him. Playing the role of seducing him to believe in her would have rubbed off on her as well.