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What about Past/Present/Future? A standard ancient-type Pokemon, maybe a fire/rock magma Pokemon representing ancient earth or culture. Something with a contemporary garb like Scrafty and finally a futuristic robotic/alien starter.
Actually I hate this idea now I've said it. Lemme try again.
Underworld/Earth/Heavens. Could work really well, and it's a basic trinity that exists in some form in most religions/mytholigies.
Fire/Ground, Fire/Dark or Fire/Ghost underworld creature. Could be overtly demonic or just themed around darkness and death without looking evil.
Pure Grass or Grass/Ground starter representing our world. Torterra already ate my lunch here, but something that represents the land/globe.
Water/Flying or Water/Fairy angelic being representing heaven or the realm of the gods. Could feature clouds heavily as a physical feature bringing in both its Water typing and its sky-based nature.