Yeah... most of the characters files go in the same order as how they ordered in their debut (for instance Melee characters get ordered based on their file order in Melee, same for Brawl newcomers, and Smash 4). So Smash Ultimate still has those numbering gaps.
There are some exceptions when Smash 4 came around. For instance,
is listed along with Lucina and Dark Pit like how they were ordered in Smash 4 since he was brought back since Melee.
are listed after Dark Pit in that same order since that’s where their files were placed when they were DLC.
and
are listed after Bayonetta and are the first characters to be created for Ultimate since they were only in Melee and had to be made from scratch.
Charizard is listed twice though. One with the Brawl characters and the other with the Smash 4 characters.
Of course, Ultimate now has z92 missing from the files, which means that someone ended up getting omitted down the line. This character was decided after Isabelle and before the Gen 7 slot (now Gaogaen).