I do honestly wonder how well Isaac did in the ballot. He clearly did well enough to get both a much-improved Assist Trophy and model, as well as his Mii costume, and in fan polls generally wasn't too far behind big fan favorite K. Rool.
I don't know if it was here, but I saw someone hypothesize once that Isaac might have had a harder uphill battle due to being from a franchise new to Smash, and would have therefore necessitated a new stages, a full musical work up, and more, whereas K. Rool and Ridley didn't have to considering they came from existing series with a lot of the work already done.
It makes a lot of sense on paper as to why all of that new content being required might have stonewalled Isaac, but that sort of falls apart when you look at Castlevania, which got all of that and more, but also which I wouldn't have pegged as being more popular than Isaac ballot-wise. Makes you think.