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:
I’m playing through Prey for the first time right now and I think it’s one of the most underrated games of the past decade, but I wouldn’t call it anywhere near perfect, either. It’s launch was very rocky, enemy AI is weird to nonexistent, combat in general has the awkward property of being reduced to door camping, and the audio is… ungodly.