While the stone possessed immense power, that power ultimately lay in the stone; if he lost it or had it stolen he'd no longer have access to the power. There was also the issue he'd discovered with Karyn that wishes made on the stone weren't reversible. Jon was dreadfully excited to experience the world of magic but he was a bit wary of making big reality sweeping changes every time he made a wish. The solution, of course, was to instead wish for magic of his own.
But how to go about it? Jon was uncertain about wishing for extensive knowledge directly, worried he'd overload his own brain with a poorly worded wish. He'd read enough Lovecraft to know that the human mind might struggle to contain certain types of knowledge. He could wish for a spellbook or a magical tutor, but he wasn't sure that was the best path forward. Based on his knowledge of fantasy and RPGS, learning magic was likely something that would take years to make any meaningful progress at, and Jon was too impatient for that. Basically, he wanted to be a sorcerer not a wizard, someone with inborn magical ability. So the easiest thing to do would be to turn himself into an inherently magical creature, right?
Of course that had problems of it's own. He didn't want to go completely random, since he could easily end up as something that was more a curse than a blessing. If he turned into a zombie he'd basically be erasing his own brain, or he might accidentally turn himself into something that couldn't talk, preventing him from using the stone for damage control. On the other hand, he was wary of wishing to become a specific creature. He knew magic existed due to the existence of the rock, but he had no clue how it worked or which creatures from fantasy were actually real. He could wish to know, of course, but that felt too broad; trying to stuff the entirety of magizoology into his head all at once seemed a risky proposition.
Presumably the stone could make whatever creature he asked to be real with it's reality warping powers, but that somewhat defeated the purpose of wishing for powers separate from the rock. It wouldn't be natural magic so to speak. Still, he thought the plan was workable as long as he carefully worded the wish.
With some trepidation, Jon held the stone tight as he said, "I wish that the following wish will not take away my ability to speak or my understanding of language. I wish to become a fully intelligent, humanoid magical entity with inborn magical powers of my own." The stone glowed white hot, before a jolt of that white mystical energy traveled from the stone, up Jon's arm and into the core of his being, knocking him out as he was profoundly changed.