There's Metal Gear Solid 4. I mean I don't like the game, but it did actually try to modernize MGS controls. Excellent sound design, incredible polish, and some at the time time high end graphics. It was a marque title.
If you mean high end Japanese games as pure production values and not quality. There's more. RE5, 6, Blue Dragon, Tales of Vesperia(I don't know, it sure looks like a step up compared to those that followed), Soul Calibur, FFXIII for sure, Ni No Kuni, and maybe the two Ace Combats?
Yeah, I guess those days are done though. Well whatever, I'm ready for my western overloads and Witcher related products.