I don't see the PWT just like it is. But perhaps a Pokemon Stadium style tournament system with different cups that involve different rulesets, complete with cameo battles and such from old characters. It can also be expanded with DLC being on the 3Ds and all.
Edit: had to reread after posting to see I left out an entire thought from the middle of a sentence. Stupid 5:30 am...
PWT got incredibly boring after the first few times, if any old Battle Facility should get back in it should be the Battle Frontier.
Are you serious? No way in hell. PWT was the best. you coulx battle all the gym leaders and champions. how was it boring
Are *you* serious? PWT was the Battle Dome for noobs. The Bug- and Dragon- specialists (Lance, Bugsy, etc.) were all outclassed by their since-gone Bug Catcher and Dragon Tamer counterparts (pool of 6 Pokémon vs. far more than that). Ditto Water-specialists and Swimmers.
The Frontier had...variety. The internal currency system of the Battle Castle, the survival instincts needed for the Pyramid, the game board of the Arcade, alternate ways to win in the Arena...need I say anymore?
Not to mention the flavourlessness of it all. Who looks after the gyms? Where do they all live in Unova? Why does no-one in Driftveil care that they're there?