Nothing besides honor. However, there is the balance between our ability to pick any 6 mons from nearly the entire pokedex versus their restriction to exclusively one type. So, success comes down to a balanced team with pokemon that can to adapt to different strategies. There's also balance in needing 2/3 wins per tier to advance in the league, so if a particular type completely shuts down your team, try against the other two leaders. Once leaders/tiers/aces are announced, you could even plan your team specifically to only deal with 2/3 teams per tier and avoid whichever weaknesses you'd have every tier. There's also the balance in the time and effort needed to create a new team per challenger. It's likely leaders will have a couple of "staple" teams with their best strategies to alternate between rather than counter picking every single opponent they have. There's also the balance that the leaders will not keep the league alive if all they do is straight up counter opponents, as they'll lose their participants if the league is "unfun" and "unfair."
tl;dr: If they really want to counter all their opponents, they could, but the time/energy/effort of always doing so would be large and not truly in the spirit of having a fun/fair event.