I believe The Beatles: Rock Band came the closest to being perfect. Eveything about that game was just beautifully done and the only things missing was Pro Drums, an option for Keys, and a few more Beatle songs (Hey Jude, Strawberry Fields Forever, Yesterday etc. etc.)
I would interpret “perfect” as “i can’t find anyhing negative to say about this game”. So for me the candidates are:
- Portal 1&2
- Factorio
- Outer Wilds
- FTL
- TowerFall: Ascension
- Dishonored 2
- Prey (the Arkane studios one)
- Minit
- and maybe Nidhogg