I know you want to encourage players to play as many tournaments as possible, so I am not suggesting that you restrict the number of games that count towards the leaderboard, but rather that you increase the number that count towards the point total to better match the number of games that people are actually playing. For instance, I am the only player in the top 50 of the high stakes MTT board who has played fewer than 30 tournaments. Based on the number of tournaments for most players, it seems like the number that should count towards the high stakes board should be about 40.
While it may seem counter intuitive at first, raising the number of games that count towards the cap actually helps players who can’t play as many. For example, Wrongler has played 140 games to get his best 20, while Bigtimer11 has only played 60 games. If the cap were 40 games, Wrongler would still want to play as much as possible to improve his position, but Bigtimer11 would have a better chance because his per/tournament average is likely to be higher, and this would reduce the advantage of players who play all the time.
I would recommend 40 games for high stakes, 90 for medium, and 120 for low.