Well, Sin and Punishment: Star Successor released around the same time when Sakurai was looking for content to add (2008), and in that game, Saki wasn’t even the main protagonist, it was Isa Jo, and it will most likely be him in the next game if there even is one (for Spoiler reasons, inconclusive ending). So I’m assuming he wasn’t planning on using Saki for anything since we had Isa as the more relevant/popular character. But this is reaching tin foil territory.
It’s still weird though because, Golden Sun nor Sin and Punishment: Star Successor get anything. I mean unlike DD, Star Successor was given praise by the media, but it just did mediocre sales.
My theory, simply put they were low priority. It’s clear from Isaac’s absense as an assist trophy and the new music track that he was planned for something else along with Golden Sun representation in general that explains this, and they weren’t able to get to it because they didn’t have enough time. This might also explain why Saki is still an assist trophy. Isa Jo and the second Sin and Punishment game came right at the time for Sakurai to consider. Naturally due to where the series was planned to be headed, Sakurai instead decided to opt for Isa and Star Successor content, but couldn’t due to time constraints, and just had Saki in there.
If this ends up being the case (which although should be taken with a grain of salt, seems like the logical conclusion) along with large popularity from the ballot, Isaac would’ve ended up being one of the first newcomers to be planned since it’s clear from Ultimate that Sakurai is addressing previous things he has considered before and couldn’t get to, with Isaac being a recent example (and even the planned Sin and Punishment content and ISA!!!). But keep in mind that this is just one possibility, and Isaac may not even be considered.
Let’s just hope for the best folks! We’ll soon find out about Isaac’s fate along with Golden Sun and hopefully it lands in our favor. And for me, along with Isa Jo and Sin and Punishment representation, I don’t like Saki though (his hairstyle is kind of dumb). Isa and Isaac have untapped potential for awesome movesets not in Smash yet. (Gun Blade? Spell Telekinetic Swordman? Why is it not in muh Smash!?)