I think it depends on the style of the game. For example, in increased difficulty Rom-Hacks, like Blaze Black 2 and Renegade Platinum, I like it, as it gives more variety, and since the focus of the games is on challenging battles, most of the time it brings attention to overlooked Pokémon and serves as a nice buff.
Now in games that have a whole new story and region, I'm not the biggest fan of it; I think it distracts from the story, I guess. And I specially dislike when a game has Fakémon and Region variants, but still changes a Pokémon's typing.