I wrote up a post similar to Black Tiger's earlier today but the internet ate it.
The GC has Soul Calibur 2, CvS 2, a bunch of (better than you'd think) Naruto and DBZ games. It also has Kinikuman, which I f*cking LOVE. Obviously that's no PS2-grade selection of fighters, but it kicks the shit out of what the N64 has; wrestling and Mortal Kombat.
Shooters are a similar thing, a small selection but vastly superior to what the N64 has (basically nothing).
As far as I can tell the N64 is loved by people of a specific age mostly because of the timing and maybe Zelda tOoT (which is hugely overrated, IMO). Those same kids who were in that perfect age bracket were also trying to "grow up" when the GC was released so they though it sucked compared to other "mature" systems like PS2 and Xbox.
Objectively the only thing the N64 really excelled at were the Pokemon games (which, without the GBC games to link with, were nearly useless) Mario, and Zelda (sorta). It really just pretty much sucked at everything else.
The GC on the other hand...while the volume of good software is low, its certainly there, and the hardware itself is great, IMO, dead reliable, compact, plays all GB games made up until that point, a very solid controller, 480p output.
The GC sometimes reminds me of the PSP. If you go to Target or wherever and look at the PSP selection you'd think that system was the biggest piece of crap ever. There isn't anything in the shops except Madden, SOCOM, and Bratz. Its hell. If you look at my game shelf at home though you'd only see about 15 games, but (almost) all of them are f*cking great. The same sort of thing happened to the GC. It took a long-ass time, but over the lifespan of the system some really great things showed up. It was just easy to forget them because they went out of print and were never seen again.
There are also a few good JP-only GC games. Mobile Suit Gundam: Senshitachi no Kiseki (aka: The Ace Pilots or The Pilot's Locust) is every bit as good than any of the PS2 Gundam games (much better than many). PCE fans would also like Bomberman Land 2, which for some reason stayed in Japan while the shitty B-Man games like Jetters were localized instead.