So let's try to take off our bias glasses for a minute. Do you think there's any chance Isaac was not made an AT because he was planned for later on?
I think there is a chance, but I also think it's likelier this has just been a fortunate coincidence.
That is something I've thought about for a while. I came to the conclusion that removing some of Brawl's ATs was a possibility, but also that there must have been a reason to remove them, because Sakurai wanted to have as many ATs as possible (at least that's what I understood from what he said in a Direct), and they were not the hardest things to port.
Isaac in particular was, with Little Mac, the most beloved Assist Trophy.
I believe that Little Mac was not supposed to be the only AT upgraded to a playable character, but they ran out of time.
Let's check out the other ATs that disappeared from Brawl to Smash 4: Drill Dozer, Excitebike, Barbara the Bat, Custom Robo, Mr. Resetti, Herilin (that padel), and Gray Fox.
At first, Gray Fox is simple to explain: Snake is not in the game anymore.
Then, there's Excitebike, Custom Robo that could have been considered for playable characters, they're decently popular (aren't they? Not too sure).
Drill Dozer and Barbara
may have been considered too, because they could be original characters from unrepresented IPs.
Keep in mind that there must be a big list of characters who were cut, and they probably didn't have the same priority. Isaac would have been pretty high on that list.
Then, there's Mr. Resetti and Helirin. They were not really useful. Some can think Resetti was funny, but even me who like Animal Crossing a LOT, sighed when he appeared after two or three times). That may be a reason to cut them in Smash 4.
TL;DR: Different reasons for different ATs. I can be completely wrong about this, though.