Well even though Isaac's popularity in Japan is not what it once was, pre-Brawl it was much higher than Saki's. Post Brawl Shulk's is much higher than Saki's.
In the west Saki is relatively (or at least comparatively) unknown, his series only had a measure of success on the VC, and both others are more popular.
Not to mention, at least with GS, that the series in terms of audience size is several times larger. Even Xenoblade's might be... it certainly fared better than Star Successor.
People like to bring up Sakurai's bias in regards to Saki... but Sakurai has never stated affinity for Saki personally or anything, and more importantly even the characters Sakurai does state he as an affinity for don't wind up included unless they have many other factors in their favour. I mean the character Sakurai wanted most in Smash since 64 still hasn't been included, and probably won't be this time either.
I don't see any area in which Saki has more in his favour than either Isaac, Shulk, or in many cases both tbh. I fully agree he'd be a cool character with a great moveset, but so would the other two, and they do have more going for them.