The best approach in my opinion was in Mass Effect.
Dragon Age a close second but there it's much more subtle and good/evil not really a part of it, it's more internal to you the why behind your characters actions. Stuff like using blood magic which is illegal but very powerful can be used from a perspective of "the greater good" or you could roleplay that decision as a lust for power. Which factions you side with for sure has morality attached but since all roads lead to saving the world its much more about your own reasons to judge if your character is evil or just focused on the grander scheme, utilitarian.
But back to Mass Effect. It's the same thing with all roads leading to save the world but unlike Dragon Age there is a morality system in place that is not about just a dichotomy between self sacrifice and malicious indulgence. Instead it's about what is OK to do to save the world? What sacrifices are reasonable? What risks should you take for others? What approach do you take to solve conflict? Renegade (as the 'evil' approach is called) options allow you to pistol whip people that want you to follow rules and decorum while the Galaxy hangs in the balance. It allows you to order people to die for the greater good. It's about using the power you have to take the shortest and most direct route to ultimate salvation. To not pussy foot around trying to appease everyone.
And really that's the only way to make morality work in a story driven game imo. If the same story is to be told with moral decisions left to the player than they need to be ultimately inconsequential to how the game and story plays out. At best they give slight variations to story beats but nothing really changes from a good playthrough to an evil one in the grand scheme. If it works and feels satisfying is largely down to the developers accepting this and instead focus on smaller nuances like Mass Effect or leaving it ambiguous and up to the player to craft their narrative for the why and motivations like Dragon Age.
What I'd instead would like to see is a game where you play out an evil narrative. And I do know of one such RPG, Tyranny, but I haven't gotten around to play it yet.
The best example perhaps of melding good and evil in the same game is Star Wars: The Old Republic (the MMORPG). Because you can play it from the evil side as a good character and the good side as an evil character. If you play it through multiple time you can really craft a world and narrative of incredible depth. And I can really recommend playing it as you would any other western RPG and just ignore the MMO side of things. Bear in mind that each individual playthrough suffers from the exact problem you raise in your post, but on the total, the bigger picture, becomes something very interesting and worthwhile.
1337x is probably the biggest these days and it just needs a free quick and easy account to upload a torrent. If you're concerned about privacy then use a mail relay like Firefox Relay which is free.