To play the devil's advocate... Isaac just has unbelievably stiff competition in the JRPG protagonist department (
![Cloud :ultcloud: :ultcloud:](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
![Shulk :ultshulk: :ultshulk:](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
![Hero :ulthero: :ulthero:](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
), to say nothing of the Fire Emblem crew.
For Shantae, the issue seems not to be a lack of potential, but rather too much of it, or at least the wrong kind when it comes to Smash 4. That game was notably anti-transformation character, separating Zelda and Sheik, Samus and ZSS and making Charizard a solo fighter. At the time, Shantae's best known abilities came from Pirate's Curse and Half-Genie Hero. But the full transforming of the latter probably wouldn't fly in the 4 engine, Pirate Gear would not have been very representative of Shantae's character and trying to heavily modify any of it to suit Smash might have been seen as doing a disservice. This situation did not change much going into Ultimate's development, sure we got the Trainer's team back, but only to fit the theme and after heavy rebalancing. Shantae probably was still too much of a hassle to consider developing in that hectic environment with her current known abilities and situation.
Enter Seven Sirens, a game that uses Shantae's iconic magic transformations but without overriding her normal moveset in the process. Now, the door is open to making a Shantae moveset that isn't overly complicated to balance, yet still remain faithful to the games. The only question at this point is how much, if any, info was the Smash dev team privy to regarding that game?