While the C-Stick was not ideal for FPS games, on an unrelated tangent, it was pretty good for a casual approach. I find that the GC controller worked really well with casual or otherwise lapsed gamers. Fingers rest comfortably on the L and R buttons, Z button - while awkward - was immediately identifiable, A button and B button's design made it obvious which was select and which was cancel, and the C-Stick stood out from the Analog Stick, so people would better understand that its functions were different. I'd personally make it bigger, but...
I don't disagree with you, but this illustrates where Nintendo's problem really were. The controller was so tailored to being casual friendly that it negatively impacted many core genres. FPS games like Halo it was unsuited for. Fighters like Tekken and Street FIghter it was unsuited for. Racers like Outrun 2 it was unsuited for.... The lack of a Perfect Dark Zero is a tiny issue in comparison to the fact that Nintendo was building its hardware to benefit their games at the expense of everyone else's. This has continued in generations since, and makes all of their platforms unappealing to third-parties.
Original Perfect Dark was kind of terrible, I hated it. Halo is notable for the improved console controls the game felt really, really good to play whereas other shooters were fairly clunky. PDZ had nothing really notable about it.
I'm not saying it was special (I enjoyed it a lot at the time though). I'm saying "standard arena deathmatch" is a pretty crappy criticism, as it can be used to describe many of the best multiplayer shooters ever to exist. At the time of release PDZ was one of the best multiplayer FPS games to be made available on consoles (I'd place Halo 2 and RTCW above it), which is why many people have such fond memories of it. Of course once Gears of War hit, its time was over immediately.