Unreal II: Aliens
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Despite what I said before, it turns out that the story in Unreal II: The Awakening isn’t simply Humans vs Alien Monsters. The third through fifth missions feature human antagonists. And, although I’ll be very surprised if there are any sympathetic Skaarj, we’ve seen a few aliens on the Terran Colonial Authority side from the very beginning, purportedly as part of an officer exchange program. One, named Ne’ban, even pilots the player’s ship. He’s basically a comic sidekick, mangling his English, being confused about human customs, and generally being childlike in comparison to the humans: short, awkward, with a higher-pitched voice. Characters like this have existed for a long time, but an earlier generation would have made him Chinese or something. I’m not sure whether an alien version is a positive development or not. It strikes me as related to the question of whether the Ferengi are anti-semitic, except less specific.
Also, although the living planet in mission 3 isn’t exactly friendly, it can hardly be called a bad guy. At least, it’s not the aggressor in the situation — that would be the morally questionable human corporation trying to excavate a mysterious macguffin from under its surface. The player doesn’t want them to have it, but the planet doesn’t care about factions — as far as it’s concerned, you’re all part of the same infestation. Hopefully it can just heal over and live in peace now that the artifact is gone, although that kind of depends on whether the corporation was solely interested in the artifact or had other ways to profit from killing a planet. It’s worth noting that the corporation has a Japanese name. Even when the bad guys aren’t aliens, the authors want you to regard them as foreign.