Nier vs Iji
Higurashi vs Legend of Mana
Final Fantasy 6 vs Fate/Stay Night - Totori & FF6 are comparable, eh to FSN.
Tales of the Abyss vs Castlevania Symphony of The Night
Bubble Bobble vs Final Fantasy 3 - I played Bubble Bobble on the Amiga, instant disqualification. (Amiga had better sound quality than the NES rendition anyway.) But yeah, BB's theme is catchy enough but FF3's boss theme is authentically good for the time.
Super Mario Bros 3 vs Megaman 4 - Weird picks from SMB3 since the overworld themes loop in like 20 seconds (as would make sense, you have no reason to spend a long time on that screen), but it's got other solid stuff. Quite unimpressed with all the linked MM4 music, MM2 & MM3 seem better than it.