Pikmin. It's a franchise about slavery, racism, and genocide. It's basically a reenactment of the colonial era, where technologically superior beings show up, force the natives into bondage and work them literally to death in order to stripmine their land in pursuit of material wealth.
Metroid as well. Super Metroid's title screen had human corpses on it, while the opening of Prime is grim indeed, as you explore the wrecked space pirate frigate, first finding mangled bodies whose cause of death your scan visor recounts in gruesome clinical detail, then later wounded and dying pirates whom you gun down as they try feeble to attack you, while your visor informs you that "this subject has suffered severe haemorrhaging of the brain, and therefore cannot aim effectively" or "subject's legs are broken, preventing it from escaping".
Prime 2 similarly details the emaciated corpses of Luminoth warriors who stayed at their posted until they starved to death, or killed themselves to avoid being possessed by the Ing. It's atmosphere is also deeply oppressive; brilliantly so, but so much that I actually found long play sessions exhausting.
Nintendo sorely needs to revisit this kind of territory, it would bring some much needed variety to their first party catalogue.
