I agree that the 3 setting should be "average" and should correspond at least somewhat to a player's real life stolen base attempts.
For some reason, though, this only seems to be the case if the player is classified as a runner. For example, I have 1990 Julio Franco in a league right now, and he's set at 3 for most games (and set at 1 when the opposition catcher has an A+ arm). Through 66 games he has 12 attempts, which works out to about 30 over 162 games. He had 41 attempts RL, so when you take into account the handful of games he was set at 1 then the 3 rating is reflecting his RL attempts pretty well.
Now, if you put a "non-runner" on 3, chances are you won't get anywhere close to his RL attempts...