i really like this idea and i think the list given in the first post of the abilities is perfect , i think only a very small amount of players should have an ability , say 3 players each draft (skill listed as a star on scout report) , if implemented give one player from every team a random ability , the abilities should be well balanced and only make a small difference to each game.
also i think the abilities should be shown as a star on the players page to all players with only the current owner of the player being able to see what the skill is. once player is placed on transfer list the skill would be displayed to all.