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 agree, Chakotay was just... there
a lot of the time. Even when he challenged Janeway she usually won out in the end. You have to wonder if he had had a little more 'oomph' in his personality if things would have gone differently.
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.
I liked Jaffen too
He was such a sweet guy, and that goodbye scene at the end of 'Workforce' breaks my heart every time.
I think too that with Kashyk it was much more of an 'events and circumstances' sort of thing combined with a sort of mutual attraction.