I think there could be a few other ways other then level-raising and more pokemon. -Random encounters, maybe increase the frequency. -Give wild pokemon a much smarter AI -Change what pokemon appears in grass. -make Trainers harder to avoid and smarter. -increase the cost of items at the pokemart
About extra save files Maybe allow trading ONLY, between two files that are post-game, maybe add some facility in the post-game area.
Also, Thought of something else too, to go with the battle frontier.
6 ) - Add stadiums, like pokemon battle revolution, and colosseum, where you battle trainers and make it to the top, Similar to the stadiums in battle revolution, there could be different battlestyles, and maybe extra stadiums post game, like a stadium representing each region, like kanto, johto, hoenn, sinnoh, and a unova stadium, it could be like a secondary optional quest, maybe there could be a gym leader like trainer in the final battle of each stadium.
It sounds similar to the PWT, but there could be more of a reward for it.
And make them rechallengable and maybe harder the second time.
For this, i highly doubt the 3ds cartridges could handle this, 659+ pokemon, 3d sprites and overworld, data and other trainers.