Shit, I forgot to mention E.V.O. : The Search for Eden! One of my all time favourite games and a sequel to the cracktastic
"4.6 Billion Year Story: The Theory of Evolution" for the PC-Engine (where you can become a lizard man and fight the devil in that one). You take on the role of some Pre-Cambrian fish, as you take on a 4.6 Billion year journey to become the marry Gaia and become the dominant species of the planet. You defeat enemies to collect meat, which gives you EVO points, which you spend on parts to upgrade your current form. Each chapter takes place at a different era of Earth's prehistory, starting from fish, to reptiles, to dinosaurs, and eventually mammals. Your supposed to eventually tier up into a Homo-Sapien by the end, but I always end up forgoing the mammal power up so I can stay as a Dinosaur the whole game.
Holy shit, Secret of Evermore. I didn't think to mention it since OP said NOT to talk about Secret of Mana, and they're essentially the same game. I don't know WHY they're the same game, since it's just this forgotten relic of the 90s that's never brought up again when talking about the other Mana games. You play as a boy and his dog, stuck in some bizarre contraption by a mad scientist that takes you across various worlds based off of moments from Earth's history (i.e. A caveman world, a roman world, and a techno future world). Your dog ends up mutating over the course of the game, taking on appropriate alt forms (i.e. caveman dog is a dire wolf, roman dog is greyhound, future dog is a robot) while the boy tiers up in equipment (going from bones and arrows, to swords and guns) and learns alchemy spells that require carrying a series of exhaustible reagents.
And when I mean this game is a relic form the 90s, I mean back when MTV had music videos relic from the 90s.
WHAT EVEN WAS THIS GAME!?! WHERE DID IT COME FROM AND WHY!?!?
Also, on the topic of games that take you across the annals of history. This game finally got a proper localization with an HD upgrade a couple of years ago (for pretty much everything but the X-box) with like, voice acting and everything, shit's cash. You take on the roles a various heroes throughout history (mostly the marketable ones like ninjas, knights, cowboys, cavemen, and robots. But there's also a contemporary time frame where you play as some wannabe street fighter, and "near-future" time frame where you play as a cyberpunk mutant with psychic powers). Each era has their own party of character to choose from, as well as a major storyline quest you have to beat. Eventually you find out everything is connected, and all the heroes get to team up in some sort of quantum nexus to stop the true villain of the story. Combat is pretty cool, and feels like a proper followup to Chrono Trigger gameplay wise (moreso than Chrono Cross anyway) making use of tactical movement and targeting mixed in with more conventional turn based mechanics.
I've got more, but I'll play it cool for now, so as not to just swamp the thread y'know? I-I swear I know more Super Nintendo games...just....juist gimme a minute....