Yep there is some discussion already going on behind the curtain about the team stacking issues. Its a tough one to crack, cause I understand theres a fine line between team stacking and wanting to play with your BFFs.
Most of the people who play here regularly know each other, have a lot of time on the server and because they play together so often tend to be better than the average person who is passing through. Also the fact that subscribers are immune to autobalance often keeps the stacks in place, but thats what people pay for so its not gonna change.
There are two solutions, one would be an automated shuffle at the end of a round if one team is totally dominating the other. I dont know how one would implement this fairly it would have to be some metric based on average score, rounds won and time to win. Very difficult to detect accurately especially with multistage attack/defend maps and would often spoil the momentum of a game which would piss people off. The other solution which I think would be useful is an admin shuffle command which allows admins to randomize teams if it looks ridiculously stacked. Of course that only helps if theres an admin on, and would only be used in extreme cases where the loosing team is leaving in droves and killing the server.
With or without these changes, I suppose a plea to players to follow Schizoid and Villans example of choosing a random team, and to ask people not to join spec after being autobalanced is all we can really do for now.