My examples may not fit the definition of AAA but here's what I got from the top of my head. Etrian Odyssey has a much more robust battle system than many bigger JRPGs, the way it handles basic encounters especially is definitely better than the competition. Cave Story has better level design than a bunch of Metroidvanias that content themselves on emulating the mediocre one from SOTN(hallways/rooms with random platforms and enemies).