It's position and layout felt off for the genre, IMO. I, for once, was struggling to get used to the Z button for firing secondary mode on games like TimeSplitters 2 and Red Faction 2.
Gameplay-wise, some of the games from the genre felt gimped because of the lacking buttons. There weren't enough shoulder buttons - although GCN's L and R buttons were great for the genre -, Z felt off and there wasn't 元 and R3 (no analog buttons). If it was a game developed with the N64 controller in mind foremost, like Metroid Prime and Geist, then yeah, it worked, but for most multiplatform FPS titles, such as TimeSplitters, Red Faction and Medal of Honor, GCN controller felt weird to play.