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SMTIV definitely. Mostly through Demon fusion, but some demons can naturally evolve, like the Angel.
Does Etrian Odyssey III and IV's Subclassing count? I know it's a stretch, but you get it later in the game and it does give your characters extra Skill Points and new abilities.
Games with Job Systems are similar to evolution. Final Fantasy V, Bravely Default, Final Fantasy Tactics, etc. You unlock new jobs as you progress, these jobs change the characters' appearance, and they get new abilities and skills from leveling those jobs.
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