In Diamond Mind I don't use individual seasons. I use their All Time Great Players discs where each player is made up based on his best 5 consecutive seasons, except if his career was very short. In that case they base him on his full career stats. Every player is normalized for era, so guys like Cochrane and Lindstrom have an average around .285 because of when they played. And Cobb is at like .380 for the same reason, as averages were very low for much of his career, so his .366 goes up.
I have made up 128 of the greatest multi-season teams of all time. When I run tournaments each matchup plays 162 games head to head. The 1936-39 Yankees are the best team and they will win the tournament around half of the time. Other teams that have won include the 1949-53 Yankees, the 1926-28 Yankees, the 1942-46 Cardinals, the 1996-2001 Yankees, and a few others. The 1942-45 Pittsburg Crawfords of the Negro Leagues have gotten to the semi-finals a couple of times.
When I run draft leagues I usually do it by decades, or with a 19th century league where any player who played at all in the 19th century is eligible.
I also have all time rosters for each team, and a league based on where a player was born, with states and foreign countries. California is the best team with Ted Williams at DH, Barry Bonds, DiMaggio and a platoon of Gwynn and Bobby Bonds in RF. McGwire at 1B. Joe Gordon at 2B, Seaver and Randy Johnson among the pitchers.