Second Wind should definitely stay. It's only one of many traits you can choose, so to use it, you have to give up something else. As @Rafa_SLB_ rightly pointed out, some players do find a bit extra near the end of a game.
I also think they should boost stamina penalties in Clubs games. Get rid of the injury nonsense, this only penalises players for a minute or so. Make it so that a player whose stamina is less than 30% gets a 30% (say) drop in all stats & less than 10%, a a 50% drop. Maybe this'll deter the pressure & sprint whores & make them think more about the entire match.