The emulation that Nintendo has on the virtual console and NES mini was painstakingly (which is why VC releases take so long) done by Nintendo (the original hardware maker) in conjunction with the publishers/developers themselves. Emulators are just not as smooth and glitch free. I use emulators for arcade games, because the glut of them will likely never hit an hd VC release, but the emulation is done per each game here, by the people responsible for the games and hardware in the first place, with the resources that match.