Well for starters, no sandbox game is truly a sandbox. They've all got pre-written stories that, one way or another, follow the Good Guys vs Bad Guys format. Quite simply: they don't want a game where the bad guys win. I'm not saying I've played every game out there, but personally I liked Knights of the Old Republic because you actually had the genuine choice of "I'm gonna be a Sith, Mother-Fuck the god damn Republic, I'm gonna take over this *****!" And sure enough you can kill your treacherous apprentice, reclaim the Star Forge, and realize your dark ambitions once and for all!
The point is that KotOR is perhaps the only game that I, personally, can think of that has a genuine "The Bad Guys Win" possibility for an ending. But see KotOR actually had a good reason/story that allowed for it to have a Bag Guys Win ending. KotOR's story progressed with you assuming you're a good (or at least neutral) guy at the start of the game, or at least there's room for conflict because the bad guys (Malak's forces) are trying to kill you. So you progress through the game and don't officially find out that you're really some ultra badass who used to be pretty damn evil. From there you're given the choice of renouncing your evil ways and becoming the shining beacon of hope and justice the Jedi's always hoped you would become...or you can choose to reclaim your dark mantle of Lord of the Sith, strike down your treacherous apprentice, and take back your empire.
With today's games, you're not given such a choice to return to a past of darkness. The game puts you in the situation of a hero and your only choice is really "Are you a true hero? Or are you an anti-hero?"
For instance, I finally got done with my Full Renegade playthrough of ME 3...annnnnnd yeah, ReneShep gets the job done just as well as ParaShep, the only real difference is that ReneShep is just the most backstabbing son-of-a-***** in the entire galaxy. Between Mordin, Wrex, and having to put Legion down like he's Ol' Space Yeller ("HOW IS THAT A THING?!"

) ReneShep proves that there's no one he won't throw under the bus and utterly betray as long as it suits his purpose. ParaShep proves that she'll bend over backwards to make and spread peace to serve her purpose. The thing is both of them have the same purpose: defeat the Reapers. ReneShep isn't trying to defeat the Reapers so that HE can control the galaxy (like Darth Revan wants to defeat Malak so that HE can control the Sith), he's just not afraid to make any sacrifice necessary to win.
In short: games that have a morality system don't really let you choose between being a bad guy or being a good guy, they're choosing "Do you want to be a nice guy on your way to achieve your goals? Or do you want to be a fucking asshole?"
I'd say the Bioshock games, though, make an admirable attempt at having Good Guy/Bad Guy endings. BS 1: Leave Rapture vs Take It Over and Become Splicer King. BS 2: Free a benevolent super powered girl who will help mankind progress to the future vs Unleash a malevolent ***** who cannot wait to to exercise her "daddy's" bloody wrath upon society.
Annnnnnnnd I'm officially starting to ramble so I'll kindly shut the fuck up now.