If a challenge mode were introduced, I'd suggest to create a second storyline and send the player to all of the Gyms a second time around, challenging much more difficult teams. The badges can be enhanced versions, like having a golden treatment to them or something. Once all badges are collected again, the final E4 of the game has something like Lv.80 Pokémon with all the extra experience you've been gaining. There can even be a new Victory Road, and you can't rechallenge the E4 until you are eligible the second time, instead of being able to go right back. New benefits can be tied to the second round of badges, and thus you can for instance have Lv.70 trades stop obeying you with all eight "normal" Badges, etc. (No using high-level Events the first time!)
It would be neat if the second storyline goes through new areas that have the much tougher Pokémon you can train against.
Admit it, you like this idea.
Cyclone