The difference with FC is that it is wired for extra sound and has an expansion port. Without modification, NES won't play the extra sound from a handful of games. However, the majority of games play the same on both systems. Lightgun games need to use a light gun from the expansion port when played on the Famicom, regardless of version (NES has the lightgun wired for port two, FC has it wired for the expansion port). Arkanoid and Arkanoid II FC are incompatible with the US Arkanoid controller since it's wired differently.
There are also a few FC games that use the expansion port for 3-4 player games. The 3-4 player modes for these games can't be played with a four score on a US system. US four score 3-4 player games can't be played in 3-4 players with the FC expansion port
