UPDATE: The game is finished!
I'll be uploading the full version soon, hopefully in the next few days.
I've play-tested from start to finish and have hopefully taken care of any errors, though I'm sure some will still pop up. As they do, I will make a list and fix the minor ones in one patch once several people have cleared the game. Bigger errors will of course take priority and receive a fix as soon as I am able to upload, not being able to do that at home creates delays.
Once you clear the main story in Shinto, you will have access to the Hoenn Region. Just like with Kanto in G/S/C, the region is downsized a bit but rather than making the maps smaller I've cut out the water routes and areas that are not really important in this post game. I did my best to recreate the maps based on Emerald Version appearance.
The Battle Frontier from Gen 3 is present and accessible post-post game but functions more like the anime, where each location has the Frontier Brain only that you will battle. These matches, save for one, require you to choose either two or three Pokemon to use against the Frontier Brains.
The "official" end of the game is after you've defeated the Battle Pyramid, with the final Trainer's levels in the low 90's.
There are a total of 281 Pokemon available to catch as well, so fill that Pokedex!