OK, about the Isaac negative points...hmmm... let me try:
-Isaac is only popular for hardcore Smash fans, and don't say "But only hardcore Smash fans buy DLC", because that's not true. Casual fans are very important to Sakurai because they are more and that means more money... and for casuals Isaac is just magic anime guy number 745, who also doesn't have a recent game to promote, like Shulk.
-Golden Sun doesn't have new games and I doubt they will make a new one soon thanks to Mario Tennis.
This matters when you consider that all the newcomers are very iconic/important to Nintendo's history (the third parties, retros, Little Mac, etc) or recent (Palutena, Rosalina, Dark Pit, Shulk, Robin, Lucina, Greninja, etc). Isaac is not really iconic or recent.
-His AT was removed and he is probably not a pre-ballot character (because veterans), so the conclusion is that he was removed because he is not relevant anymore.
-The Golden Sun music sounds in random stages (Norfair and Palutena's Temple I think), the music sounding in other characters's stages is something negative IMO, for Isaac and also for Rhythm Heaven characters.
Isaac is like Ness, but Ness was included in the first game thanks to HAL bias, making him and his franchise more popular and a staple in the Smash series. But yeah, this is just my opinion, and if Isaac has a lot of ballot votes, it obviously can happen.
I think he has 40% chances.
Also remember that the ballot is a suggestion box, the characters with more votes like K.Rool are not a shoo-in, sadly.