The inspiration for much of my statistical work, Advanced NFL Stats, has a game prediction model that uses team stats to predict game outcomes. A similar effect can occur in football as in Team Fortress: teams that face relatively easy schedules early in the year can rack up some very good numbers. A solution to this problem is to adjust a team's stats to reflect the strength of the teams that they played when they got those stats. Teams that faced weak opponents have their numbers docked slightly for their easy schedule, and those that faced much stronger opponents are boosted.
The problem is exacerbated by the way most 6v6 match-ups are being played. Pick-up games and lobbies have players of greatly differing skill levels coming together randomly for one game, and then those particular teams never face each other again. Since the strength of your teammates matters just as much as the strength of your opponents, we must also adjust each individual's stats by accounting for their teammates.
I'm currently working on applying an Advanced NFL Stats-style model to Team Fortress 2 games. I'll be using the technique of adjusting for opponent strength, and also extending the technique by including an adjustment for the strength of your own teammates.