While individual conflicts often have more clearly defined heroes and villains, almost every major faction in the BattleTech universe is ultimately like this, and many characters are simply soldiers and commanders doing their job for their respective cause.
The only faction that could truly be considered evil was the Word of Blake, and they didn't become true villains until 20 years after the setting premiered.
Exalted. While the various demons, undead, and The Fair Folk are usually portrayed as antagonistic (and even then, there are exceptions), the various human and Exalted factions all have plenty of good people mixed in with the villains, selfish bastards, and crazies.
The closest things that the setting has as out-and-out villains are the Neverborn and the Ebon Dragon. The first are a number of undead gods, always dying and suffering, who desire that everything be swept into Oblivion to end their torment. The latter is the spirit of opposition, who is -everyone's- antagonist and whom most believe to be evil because they believe themselves to be good.
Planescape. Factions aren't explicitly good or evil, they just have different motivations and can commit a variety of acts.
In the Dungeons & DragonsWrath of the Immortals campaign, the two principal factions of Immortals (D&D's functional equivalent of AD&D's gods), the Ring of Fire and the Fellowship of the Star, both have good reasons for what they do, and both pursue their objectives by morally questionable means. Rad and his followers in the Fellowship of the Star are just pursuing knowledge, and are studying a magical artifact, the Nucleus of the Spheres, that has incredible powers that are unique in the universe, and might possibly be used to make the world a much better place. The problem is that the Nucleus is draining the magical energy from the world, which would, among other things, exterminate every magical race, including elves, dragons, fairies, etc., meaning several counts of genocide. To say nothing of all the other people who would die as the civilizations, most notably Alphatia, that depend on magic would collapse. So Ixion and his followers in the Ring of Fire have sound reasons to want to destroy Rad and stop anyone from using the Nucleus of the Spheres. As things develop, however, the only way to destroy Rad is to kill all his mortal followers, meaning that Ixion and his allies have to provoke a war by Alphatia against Glantri, a war which drags in Thyatis and the Heldann Freeholds as well, and which ultimately spreads to many other countries, killing millions. But neither is side really wrong. The Brotherhood of Shadow, a third group of Entropic Immortals who are just trying to prolong and exacerbate the conflict are straightforwardly evil, except that their scheming is both pretty ineffective and, even more importantly, enables the heroes to figure out the whole plot and save the world. So the good Immortals unleash a war that kills millions of innocent people, while the evil Immortals are relatively ineffective at making things worse and inadvertently save the world. Go figure.
Lesser Shades of Evil. It's in the title, people.
The three core factions of Mobile Frame Zero have varying motives but there's no designated Evil faction: the Solar Union is trying to maintain order, the Free Colonies mostly want to get rid of the Union to be free, and the Ijad are trying to protect their (actually reasonably benevolent) religion. Even the Puppeteer Parasite side of the Ijad is downplayed to make them more sympathetic, since they're looking for willing symbiotic hosts or unintelligent beasts of burden rather than enslaving humans. The core rulebook also has a Fanwork Ban that insists all factions be pursuing a reasonably defensible goal that can be achieved with negotiation, authoritarianism and anarcho-capitalism cannot be shown positively, and absolutely no Nazis or Nazi-inspired mech names ever, to encourage homebrew factions to further this trope.