Well I guess I wouldn't because like
>>35189764mentioned it's not something the company wants to do with games.
I guess you could go with some sort of Shadow Lugia situation where the legendary was specifically created as a Shadow mon. But then you could argue that the real villain is the person who created it, and the player's efforts would revolve around curing it or putting it out of its misery.
Now for some misconceptions:
>GiratinaStated to be violent, not malevolent.
>MewtwoLashes out at the scientists that abused it and in the movies it's either an anti-hero or reforms.
>DarkraiThis is more or less the only "evil" legendary we've gotten. In-game it's stated it doesn't create nightmares out of malevolence, but it's still canonically responsible of at least two deaths due to its power. And I'm pretty sure it's usually a villain in side games.