On the plus side, PC games actually enjoy the vast majority of exceptions and subversions when it comes to Native American tropes (i.e. there actually are some,) and some of the best of these come from strategy games.
Sid Meier’s Civilization series, for example, has long included at least one playable tribe, and Civ V includes the Iroquois as a playable civilization. While their special ability to travel through forest tiles as though they’re developed roads dips dangerously close to stereotype territory, it’s made up for by a respectful and informative introduction — and the satisfaction that comes with teching up to tanks and nukes before the Europeans even get around to landing on the continent. Oh, to see the look on Columbus’ face…
The Natives have a thing or two to teach the clueless colonists.
Meanwhile, Sid Meier’s Civilization IV: Colonization goes out of its way to be respectful to natives even as it simulates the act of stealing their land. At least it makes it possible to ally with the many tribes and coexist peacefully… though that’s generally done by converting them to Christianity.
Age of Empires III’s Warchiefs expansion also wins points for including separate factions for Iroquois and Sioux. Not to be outdone, Empire: Total War includes five different playable Native American factions in its Warpath Campaign expansion: the Iroquis, Cherokee, Huron, Pueblo, and Plains Nations. Actually differentiating some of the vastly different civilizations found across an enormous continent seems like it should be a low bar to clear, but it stands out against the more common alternative of just throwing in some teepees and totem poles and calling it a day.
Prey provides the most unique mix of stereotypes and subversion. Domasi “Tommy” Tawodi an involved character arc — by FPS protagonist standards, at least. At the beginning of the story he’s hanging out in a bar bitching about life on the reservation, which threatens to slip into the slightly more modern cliche of poverty and alcoholism. Most of the older stereotypes are offloaded on his grandfather, who later serves as a literal spirit guide. By the end he’s begun to embrace his cultural heritage a bit, though in this case that includes out-of-body ghost walking and a spirit animal necessary for solving puzzles. So no, Prey isn’t exactly a shining star of enlightened cultural awareness, but it does at least treat its characters like actual characters, rather than part of a backdrop that serves to announce a Western setting in the same way a plywood cactus might.