N64 emulation is horrible compared to other systems of it's era. The reason it's horrible is because the emulator authors hacked a lot of 3d functionality instead of emulating it properly, like mame. At the time it made sense... computers could barely run n64 games. But now n64 emulation progress is non-existant and we are still left with those hacks that were functional, but take a bit of effort to get working and aren't always stable.
Emulation isn't seamless on any of the consoles unfortunately. I tried to get such a thing going on the wii, I even went so far as to write several of the tools that allow VC injection as the VC interface IS seamless. The problem is once actual emulators started showing up on the wii, nobody wanted to fool with injection and emulators on the wii are just like emulators on any other console.... inconsistent interface, buggy.... lacking features, ect...
CoinOps is the closest thing out there. XBMC tried to unify things before that allowing other programs to be launcehd from within it, but the emu authors have to cooperate and unforunately emulators ported to consoles are generally hacks done by people other than the orignal authors.
A PC, unfortunately is still the best option.