Paper Mario released on N64, picking up the "Mario in an RPG" thread and starting a series proper.
Super Mario RPG was a collab between Nintendo and Square. Square famously jumped ship after Nintendo ditched the CD format. As another mentioned, Paper Mario was supposed to be the spiritual successor to SMRPG. Even though Paper Mario was a modest success, I still consider it a miss on matching SMRPG's quality bar for an RPG.
In addition, Square still held a bunch of specific legal rights around it, which is why Paper Mario was branded as being distinct, even if it had a lot of obvious commonalities.
Great game (and sequels) but it wasn't released in Europe for example. Nintendo always did these strange business moves that made no sense yet they always prevailed. For example they had everything needed to connect DS and Wii - never did. Online shop? Dead for years, etc.