Castlevania 3 sounds quite better on FDS indeed, but cartridge Metroid is by far the worst case of this in my opinion.

Part of the soundtrack is missing channels that contribute to the main melody. Even the now iconic item fanfare was barely recognizable in that version.

Also of course there’s the fact the FDS Metroid had actual saves on the disk, and they just didn’t implement them in the cartridge version, unlike Legend of Zelda. Instead we got that painfully long password system.