While I understand why everyone wants Final Smashes to be perfectly balanced and viable for tournament play, it's simply not going to be the case. It should be remembered that it's SUPPOSED to be a comeback mechanic. Not to mention that "Pity Smash" is a thing (if you're doing terribly in a match and Smash Balls are on, you can automatically attain one for doing so bad after a respawn). The entire point of the mechanic is to emphasise how strong the characters can be, and certain characters are objectively stronger than others, or at least have an ability that is objectively super powerful.
They only way I think it can be made fairer is that the better a Final Smash is, the more damage the character has to do to the Smash Ball to break it. This also means that the Smash Ball would not have a single health stat, but would instead read the damage taken from fighters individually, and not collectively. However, I doubt they would do this.