I guess it would be NieR Replicant but with the caveat that I ended up deciding NieR was my favourite game on the grounds of being the game I think the most about.
Kingdom Hearts 2, no question. It's been my favorite pretty much since it came out so that's not even counting the additions we ended up getting in Final Mix.
Paper Mario 64, literally the perfect game. (I do have some complaints but they're so minor that I genuinely don't care, the game just makes me so happy every time I play it.)