The first practical application of this was updating Sky Editor's starter editing project to replace placeholder Pokémon portraits with the default emotion. This makes it so that when one plays the game as a non-standard starter, the game no longer shows emotions like surprised without the face of that Pokémon.
The next practical application that is planned is to start substituting certain story-related models. For example, right now, when a non-standard Pokémon sleeps in a bed, the default attack animation is used instead. The player Pokémon just can't get a good night's sleep apparently. I hope to change that soon by substituting that animation with the sleep animation used in dungeons. If model behavior in Ohana3DS is any indicator, things should work out well. That is as long as the correct animation is used. Things can get amusing if the wrong one is used:
A Zorua, using Riolu's walking animation
While seeing this in-game will take more work, I've have a new build of Sky Editor that comes with support for extracting pokemon_graphic.bin with all the filenames. This is only useful for researchers or those who want to play around with models with Ohana3DS or SPICA or something. Basic instructions can be found here, and look for the new PsmdPokemonGraphicsProject project, which can repack the pokemon_graphic.bin file for anyone who's brave enough to try manual model edits. Download it here.
[Edit] Updated the build link to fix a memory leak. I don't think I mentioned it before, but you'll need 1-2 GB of free RAM because using all the RAM makes things go like 10x faster. I didn't do any actual measurements, but that's what it feels like at least.