Nostalgia is an awful beast. I still play Perfect Dark quite often with my friends, friends who used to play the game as well. When I show it to new friend, they hate it. As well as they should, it's an awful game by todays standards. But we all still love it.
Controls, graphics, and UI are massively improved these days. Let's face it, the late 90's and early 00's were not the heyday of great 3D graphics, and the N64 controller was something you got used to dealing with rather than something you would pick from a lineup.
[1] This looks pretty rough, and coupled with the N64's controller not being ideal for FPS, it's pretty much unplayable if you didn't play back then.
Also our understanding of UX and psychology as applied to video games has improved. Developers now hire people who are formally trained in architecture and form and narrative and psychology and flow, instead of kids who were quite handy with computers.
