The main issue with the N64 titles is that they came out when 3D games were in there infancy. They came out in 1999. It is now 2013 and look at games today. If the N64 titles were remade with current graphics and controls, they would likely be the pinnacle of modern classicvania. No shimmying. No QTEs. Just platforming, instant death pits, poison rivers that result in instant death, fall damage when you fall from a great height, etc.
It looks aged, indeed, but it's saved to my eyes because the aesthetic is very CV, and because of emulators and HQ textures allow me to play it "kind of" in HD nowadays.
I kind of hate old 3D, but there's some exceptions. With 3D, to me it seems like when 3D was in its infancy, games were made with great ideas and great gameplay, as when 3D evolved and allowed us to have beautiful graphics instead of giant polygons and primitive textures, it's like developers opted to have shallow gameplay. No more jumping from plaforms to platforms, no more death pits, no more open world...
There's a lot of excellent games today, like Bioshock and The Last Of Us, and MANY JRPG's... but I'm still waiting for that great modern 3D game with beautiful graphics and real platforming.