I would say Final Fantasy, for the sheer depth and breadth of its compositional variety. Mega Man and Metal Gear tend to stay well within the limits of their respective ideas (Techno Beats for Robots, Marching Band stuff for Military), while Legacy of the Wizard, Zelda II, Doki Doki Panic and Ultima III are interestingly done but do not have that many different tracks to assess.
Final Fantasy I has 21 separate tracks, in total. That is kind of a lot for a NES game of 1987, and it never seems to waste a track. Each song is specifically used for a purpose, throughout the game, and the songs that it does reuse are clear as to why they are being reused. The Castle Of Ordeals and the Northwest Castle may have battles to fight in them, but they are in fact, Castles. Matoya's Cave, the Dwarf Cave, the Waterfall Cave and the Ice Cavern are all caves which don't necessarily have any kind of oppressive strategic placement or weather condition in them.
The Marsh Cave, in particular, is never reused from when you encounter it at said location, until very late in the game at the Mirage Tower, and its focus on a somersaulting and very sinister sequential pattern makes the same point both times; you're in danger of getting lost in here. Watch where you're going.
It's got variety of themes, and uses them well. That's really all you could ask from a soundtrack, and the fact that it was done in 1987 is just impressive on the face of it. Even JRPGs of the time (Dragon Quest, Phantasy Star) really didn't have quite so much variety to their themes. It tends to make FF1's world seem a bit more vibrant and alive.