Ro Laren/Chakotay would have been interesting, but I agree that Sam suits his wish for a family better. I think their personalities are better matched, too. Also, there's the conflict between the Starfleet officer and the Maquis commander (or at least I suspect so, since you said they don't get along all that well in this AU). And now I must shut up, before I start ranting about all the opportunites for drama and character development the writers lost when they made Starfleet and Maquis best friends right from the start.