That is true, but I think it wouldn't be too hard to add some simple "idle" animation to the custom Pokémon. Even leaving out their animation entirely wouldn't have a large impact given the majority of Pokémon we see are normal ones. I definitely agree that Gen 5 style would fit the game a lot more, it would also make implementing shinies easier given we don't have rips for every Gen 6 shiny yet.
Creating Gen 5 style animations for the custom Pokémon would be a lot easier as well, the only issue I could see would be with the few Gen 6 Pokémon/Megas that are implemented given they are mostly still Gen 6 model images. But they already feel like a little bit of an anachronism.
If it were to be implemented I agree it should definitely be a togglable thing though, the only problem there being that it would increase the game's file size unless everyone used the new, updated sprites but animation was turned off. All-in-all the benefits definitely outweigh the negatives. Further down the line it would also be interesting if we could get Gen 5 style camera movement options in battle scenes but that's a far heftier task.
The issue I have is, right now, the battle system feels so far behind the modern Pokémon games. With the game's overworld itself using a spriting style similar to Gen 4/5 for which the custom sprites look gorgeous the battle system being so very static almost damages the experience. it sort of feels like you're playing Pokémon Battle Simulator.