Chakotay - "We've lost Commander Chakotay. Duplicate or not, he was real to me and he was a fine Starfleet officer, and he was a friend who wasn't afraid to let me know when I am wrong." - This is the most endearing quality about him imo and which helped save him from being simply Commander Obvious. Janeway was very often a brick wall made of her own will, and even Tuvok couldn't change her mind.
I think Chakotay was exactly what janeway needed on that perilous journey back home, not just a Yes-Man but as she said, a friend who would follow her through thick and thin, but who would also stand up to her when she was being a bully.
I didn't see the same type of thing with the other CO/XOs. I liked the potential here.
Kira - "Major, when you're with the Romulans, try to be diplomatic."..... Kira: "I'm always diplomatic!" - She could be a little annoying at times, but she would always fight on even though she had a lot of knocks in her life.
Riker - The Beard.
T'Pol - "The Captain's behavior is becoming increasingly illogical, even for a human." - There was that interesting potential for an XO which really didn't get 'on' with the Captain, something like Riker and Jellico. I really liked the potential of the Vulcans not only seeing themselves as superior, but how the attitude was portrayed and it felt that early T'Pol was going to be quite good.
Spock - "I have been and always shall be your friend." - I have to rank Spock last because out of preferance he could only work with Jim Kirk, that relationship was totally intertwined with Jim and since I assume our prefererance can include who we could feel our own XO could be if we were in the Hot Seat... then I'd say Spock could only be Kirk's. lol
Pretty ludicrous I know, when you think about Chakotay, lol, but there it is.