The idea of two games to negotiate for resulting in a lower amount of content would be much more tenable if Street Fighter hadn't shown up to Ultimate with an additional character, AT, music, and spirits.
I think it's pretty obvious that Nintendo was not afraid to allocate a substantial budget towards filling Ultimate with content, which in no small part went towards third-party negotiations. As such, the dearth of FF content can only be attributed to stinginess, the question just comes at whether it's purely a monetary thing, or there are actual (seemingly arbitrary) restrictions on the quantity of content that can be shared, at least from some IPs.
I mean, past the lack of AT, sprits, music, English VA, etc. Cloud doesn't even show up in any cutscenes. There are obviously exceptional rules tied to his appearance. In particular, I can't get behind there not being some weird rigid dogma at play with SE and music. For example, if Hero had only two other alts, I'm convinced we only would've received six pieces of DQ music.
Some companies just have odd hangups. TPC doesn't allow for Pikachu's ears to be obstructed. We still can't get Sugimori art. They were even weird about the Pokemon cries in SMM for a while. I wouldn't be surprised if SE had some weird-ass rules for FF as well.