An awful lot of oWoD and nWoD games other than Vampire: The Masquerade feature bad guys if we go by the "don't harm innocents and leave the world better than how you found it" definition. In most cases (including Vampire) they're being struggling against doing that damage, by default (usually with a later splatbook where they can simply lean into it), but they are doing it. I didn't really regard my main Werewolf character as a "bad guy", but like, not everyone he ripped to shreds was an intentionally bad person, sometimes they were just in the wrong place at the wrong time (I mean, usually a very wrong place, like a Pentex facility, but still).
Exalted has you pretty much always being some kind of bad guy. The odds of you leaving the world better than you found it and successfully not harming innocents, especially as a Solar, are pretty low, especially with the oft-overlooked Limit Break mechanic and the Solar Flaws meaning it's just really a matter of time before you go on some kind of rampage. And a lot of Exalts just Bad People - I mean, I'd say Dragonblooded for sure, but they have hordes of defenders (I mean, if they're good guys, so is the British Empire and no it isn't), Abyssals, Sidereals (OH MY GOD they're worse than Solars!), Infernals, etc.
So yeah Exalted, absolutely stuffed to the gunnels with people who think they're doing the right thing but are either horrible monsters, brutal overlords, just ticking (nuclear) time bombs.