This isn't really suggesting they should or shouldn't add this to the games. I just thought I'd ask and see what everyone would think about having Pokemon like these appear in the games.
I was looking through some of the Bulbapedia pages when I noticed on Tyranitar's page that in one of the manga, there was a unique one called Black Tyranitar. This Tyranitar was apparently far stronger than a standard Tyranitar and is considered a Legendary Pokemon. What if we were able to encounter Pokemon like this in-game and capture them?
My thought is that it could work like the forms/formes do now, like the Spiky-eared Pichu. Even if it is the same species of Pokemon, they could give it a different sprite and change its stats. While a standard Tyranitar's base stats are 600, Black Tyranitar's might be 650. Allow it to breed with the standard Pokemon in its species, but not pass down its unique-ness. (Example: Say you breed the Black Tyranitar, you'll get a Larvitar that will only become a standard Tyranitar, kinda like Manaphy and Phione). This would limit the moves it can learn because it can't learn any egg moves that Larvitar can, giving people a reason to choose to stick with the standard Tyranitar if they want those egg moves, like Iron Head and Thunderpunch. This keeps standard Tyranitar from becoming pointless. You'd have to choose between the higher stats, or a potentially better moveset.
Another one most people should remember from the anime is the Crystal Onix. It was unaffected by Water, but weakened by Fire. (Which seems to make it more like a Steel type). How about a Pokemon like that, where the type is different? (I saw someone suggest a Delta kind of thing from the TCG somewhere else, but having many Pokemon that aren't what their types are supposed to be like that would be far too confusing I think for the main series games, especially if they don't look different from standard Pokemon.) I personally like the Black Tyranitar idea better than the Crystal Onix simply because there's more differences between them and the standard forms of the Pokemon, but I thought I'd add it anyway.
(Another I'll just mention that I liked was Shadow Lugia from XD. Not sure how they could work that one in because Shadow Pokemon don't exist in the main series games.)
Would this be interesting to anyone at all? This was just a quick thought so if anyone has any ideas to add to this, please add them!