Working on him likely started at a point far enough that Sakurai had doubts he could pull all of it off.
Doesn't necessarily have to be the very last character they started working on and moreso that he might have taken a while due to all the models and there was a chance they couldn't finish before the game's release.
That is not how Sakurai operates.
Whatever comes first on Sakurai's project plan tend to stick without much change, with very few exceptions;
- Dr. Mario, Young Link, Ganondorf, Falco, Pichu and Roy are all known to have been come up with later to pad out Melee's roster.
- You can also make a case for Ness in Melee as well, since the original idea was to replace him with Lucas from Earthbound 64.
- Chrom was initially planned for Smash 4 but he ended up being replaced by Robin because he felt more interesting moveset-wise.
- Dr. Mario (again), Lucina and Dark Pit were originally alts before being promoted to having their own fighter slots as clone fighters.
- Technically speaking, Sonic was added later during Brawl's development, but that was a case of him being in the initial project plan, Sega saying no and then changing their mind later on.
Any time Sakurai went off-track with his project plans, it was either for clones or to replace a character with someone else from the same series, and Bowser Jr. fits neither of these categories.