Chakotay having "good friends" may well be a thing of the past at the end of "Caretaker" already, and certainly at the end of "State of Flux". He's two words short of a mutiny at the best of times, and then it turns out that at least three of his supposed best buddies were out of control and working at cross-purposes all along: Tuvok, Seska and Suder stand out, but there may have been more waiting in the shadows.
Favoritism would add to his woes significantly - especially if he directed it at the wrong people. Out of the whole lot, Chakotay is the one least likely to take risks, and one of those likely to calculate his moves several steps ahead. He would probably calculate it an error to make life easy for yet another Person Who Betrayed Chakotay (TM).
Timo Saloniemi