The only gyms that will be difficult is using cut at Erika's along with Koga and Giovanni. There's nothing stopping us from picking up some new pokemon that will be more effective....Im happy that they finally beat the ledge, but I think, on some point, they will not be able to make progress, because they only leveling up two pokemons.
Also, they can run into problems, when they reach the level cap and the pokemon not longer listen to them.