The question is interesting nonetheless. I doubt Game Freak would create a game where the ending basically goes "Oh, by the way, of all the challenges you've done, this was the last one and the game is over. Roll credits!"
The Pokémon League is actually a pretty fair way to end a Pokémon game. A gauntlet of five difficult battles, the last of which is a six-on-six battle against a varied team of strong Pokémon. It is, essentially, an endurance test of the mechanics and team building you've been practising the entire game. The Pokémon League is the "end boss" of the games, preceeded by the game's hardest dungeon (Victory Road) and a saving/resting point (The Pokémon League Poké Center, which you can leave and return to whenever you want). The Hall of Fame is your victory cutscene, a definitive "now it's over, you've beaten the game" before the credits roll.
Gameplay- and mechanics-wise, the Pokémon games boil down to dungeon exploring and Pokémon battles. A near-universal rule of game design is that the finale should contain a test of the skills the player acquires throughout the game. Therefore, I think that conceptually, the Victory Road - Elite Four - Hall of Fame approach is the one feasible way to end a Pokémon game. A difficult dungeon, a save point (Fly location) for easy access after your final preparations, and a series of difficult Pokémon battles. The final battle is against a very strong Trainer, followed by a small celebration/acknowledgement of your victory.
With all this in mind, we should ask ourselves: How can Sun&Moon have a proper ending without a Pokémon League? First things first: There has to be an end dungeon of sorts, a parallel to Victory Road. This serves as a build-up to your final challenge, and is filled with strong trainers and strong wild Pokémon. An endurance test, if you like. For how long can you keep your team "alive" without healing? After the end dungeon, I think a Poké Center is mandatory. You might want to swap around your team, stock up on items, maybe even catch and train entirely new Pokémon to take on the final challenge. The location of the final challenge should therefore be easy to leave and return to, via Fly or the relevant Poké Ride. Then a barrier, a point of no return, followed a series of battles. Four (or so) difficult Trainers to wear you down, then a final battle that can only be initiated when the "minions" are defeated. Pokémon battles is a core element of the games, and this is the battle where your skills are put to the test.
All in all, I think the ending of Sun & Moon will look a lot like the ending to other Pokémon games. If not on the surface, then certainly if you judge by the actions you take. The same design elements will probably be present: Final dungeon filled with strong trainers, save point, gauntlet, final battle, celebration, credits.
Personally, I'd also prefer that the main story is over at the point of the final challenge. The Elite Four will usually represent a jump in the level curve, and require great preparations that may involve a lot of grinding. They don't present a sense of urgency, however. You're never in a hurry to battle the Elite Four, you're given ample time to prepare, explore the map, train entirely new Pokémon or just mess around before you take on the final challenge. Putting a "time limit" on it in-universe, but not mechanics-wise, creates a disonnance that breaks immersion when so much preparation is required. At least it doesn't take as much time to prepare for and return to the other "boss battles" in the game. Even if the player character is in a hurry, you can quickly return to action after being knocked out, and try again before the villain gets time to execute his final plan or whatever.
The final challenge is also repeatable, so it doesn't make sense to end with the villains. They're supposed to go to jail/be exiled/learn the error of their ways/otherwise go away after you defeat them, so it would be strange for them to still be there when you return after the credits. BW1 had an interesting approach here, with the Elite Four challenge going forward as usual, but the villain stepping in for the Champion in the initial encounter. In all subsequent Elite Four runs, the villains were nowhere to be seen.
Then again, the endings to Pokémon Colosseum and XD both broke the previous two rules quite hard, so I guess it could work either way. They included the villains, had a sense of urgency, and no Hall of Fame. There "battle gauntlet" was also absent, if I remember correctly.
But yeah, Sun and Moon. No matter how they do it, I predict there will be a big, final dungeon. Then a last Poké Center you can fly to. Then a series of battles with no healing machines in between (only Items you've stocked up). Then a final battle against an extra-powerful trainer. Then a cutscene before the credits.