I wonder if something like this would work for a future game:
>Standard Post Game area with battle facilities
>Gym Leader, Rival and Elite 4 Rematches
>Legendary Hunting, etc..., all the normal postgame stuff you expect
>New Game+. Once you beat the Elite Four you have the opportunity to restart your game with a new character (or indeed the same character if you like how he or she looks). Doing so locks all your Pokemon into a special section of the PC that can only be accessed once you win the Championship again. This allows you to play the game from the start with a fresh character.
>When you start New Game+ you have the option of releasing your Legendaries, which allows them to be caught again (and rerolls their Stats as well). Otherwise they don’t respawn.
>Most importantly, New Game+ offers Challenge mode, wherein you can choose certain special rules that you have to follow. These include Monotype, 1st Catch per Area, No Free Healing (you can only heal at Camp Sites or with items), No Champions (any Pokemon registered in the Hall of Fame from a previous run cannot be used), Natural Moves Only (no TMs or TRs). You also gain access to increased Difficulty settings too. You can take on multiple challenges at once to create restrictive, high difficulty runs.
>Each time you beat the game, you’re awarded Champion Points that can be spent on very special things, primarily on changing TRs into TMs, which is persistent across all game saves, or maybe by turning Pokemon shiny or offering some other visual change. Accepting Challenges allows you to increase the Champion Points you're rewarded with, but if you abandon a challenge before you beat the Elite 4 you void any extra Champion Points you’d gain for that run.