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pgt: I agree also. The only reason I could think that someone would not want their opponent to use autopass is that they are trying to win on a time-out, and just waiting until their opponent goes off-line to make their move. (Which defeats the purpose of playing games why you try to win by no playing games - but whatever.)
I don't see why it would be a problem on Fischer Clock games - I mean if I make a move, and my opponenet's move is auto-passed back to me - I just make another move. I mean what would be the problem? (Other then if someone was trying to win by timeout which again defeats the whole purpose of "playing" games in my opinion)
As for not using autopass if their is an in-game message - I would even be for an option of "use autopass even if there is a message" - I mean I'm going to read the message the next time I visit the game - what does it matter if it is on move 40 or 52 after 12 auto-passes? I still read it at the same time. Maybe a quick note of "Opponent had not move, so autopassed back to you - so they have not read your message yet." [again, option since some may not like that]