It's not not necessarily SE, Final Fantasy rights are just a mess. I don't know the whole story, but apparently different aspects are owned by different people, So Square Enix owns the games, but one guy owns the music, and another guy owns the artwork, etc. Dragon Quest, on the other hand, got the standard for DLCs, but the sole exception f the music. The DQ composer owns the music and is a real pain in the *** about it, apparently he's not that pleasant of a guy in general. SQ gave Nintendo the rights to two Spirit Events as well, adding up to a total of 14 characters represented between them. It's mostly that SQ's main series were just really unlucky.