It's funny how we remember the games from the early years of a console over the more polished final ones, even when trying to choose "best of all time". Perfect Dark improved on Goldeneye in every way, but rarely makes such lists (and similarly with Majora's Mask). FF6 and Chrono Trigger were stunning, pushing the SNES far further than one would have imagined possible - but it's FF4 you hear people rave about. And sacrilegious as it may seem, I think FF9 actually improved on 7 - but it's far less remembered than that first, stumbling foray into 3D, FMV and all the rest of it.