A bit late but still in time as it’s still December (and 2018) while I’m publishing this. 😅 Anyway, this time there wasn’t much difference between the two apps.
The main difference this time is that the Famicom app got (for obvious reasons) the Famicom Disk version of SP Metroid instead of the cartridge version. So you have enhanced sound effects in the Japanese version compared the NES one. (Including Ridley sound effects whenever he’s hurt)
Besides that, the differences are simple. Adventures of Lolo levels seem to be harder in the Famicom and SP Dr. Mario starts from a slightly different save state due to the random nature of the game.