When Jon wished for something interesting to happen, he didn't know what he wanted. It was a stupid wish, and it stood a big chance of blowing up in his face and going horribly wrong, and it borderline did. But he did know what he didn't want. He didn't want to be Alfred. He wanted to be Batman. He was the owner of the stone. Why on Earth would he relinquish himself to a lifetime of servitude to his sister as a stupid witch's familiar? He didn't even like his sister. He certainly didn't want to be her slave and toy, to call her mistress, to do her bidding, to be ready at her beck and call, to not really have a life of his own, to live his existence vicariously for her.
So this whole scenario, while interesting, and enough to make him want to see where it was going for the sake of curiosity, the prospect of it still really sucked, honestly. If only it was a more fair and equitable relationship with his sister, he could have stood for that. That might even be fun. But he didn't want to let this go on for too long, because there was always a risk that his sister would get some major leverage over him that would leave him at her mercy. For now, he had a way of breaking her control. And he was going to use it while he still could. And he really didn't like her attitude. This "I'm a witch and I can do whatever I want to you" attitude. And the apparent state of the familiars living under the thumb of the witches to such an extent that they weren't even allowed to have the friends of their own choosing, namely other familiars of other witches at their own discretion, them having to tiptoe around and communicate in secret, under the threat of horrible curses from the witches and councils. The familiars were definitely being oppressed by the witches, being bound to them, and abiding by their own petty politics. As the 'club' he had formed with Damien and Trevor was perhaps the first step in rebellion, in breaking that subjugation, Jon was uniquely in a position to break it further, or demolish this entire system if he wanted.
But at the same time, he realized that she wasn't taking everything from him. She might even be giving him something comparable to what she was taking away, by making hm her familiar, giving him powers of his own. She wasn't turning him into a pet, she was letting him have his life to an extent, to continue going to school, and continue living as he was with a certain amount of autonomy. Before he learned the truth, he resented that she had just changed his biology without his permission, but now he knew that in this alternate reality, his body had been retconned to be part cat all his life (even though he had been human until he had wished for something interesting) and the only thing Zoe had done was break the illusion hiding it from everyone including himself, and then given him the means to continue hiding it from others, and potentially continue living his earlier life as if nothing was different, depending on the amount of influence and control over his life she intended to impose. She had said in uncertain terms that she was going to expect him to be living a life of servitude later, to an unknown degree, depending on how much she felt like exploiting him, or maybe she was just teasing with him because he had just been very mean to her on her birthday without any provocation, and she could have done so much worse to him. Maybe he should have at least taken her birthday as the one time to be kind to his sister. So for the moment, it seemed right to give her the benefit of the doubt. So it didn't warrant retribution or a reversal. She had power, and was at worst not using it too badly. And that deserved him returning the favor at least. And apparently being a familiar meant he had powers similar to hers, but apparently male witches were less powerful and that was the origin of their oppression.
So in line with that, he didn't really want to screw too badly with what she had going for her now. Just to take the edge off. He wasn't going to flip the script and make her into his servant, he just didn't want to be at the witches' mercy as basically just the less talented help, the Alfreds to the Batmans. So the answer was clear enough: just wish to boost his magical capacities. If for no other reason, just to throw a wrench in this status quo that the witches had going. They were too comfortable in things being the way they were with them being on top and calling the shots, they should be knocked down a peg or two. But how far should he go with this? He didn't want to wish to have godlike powers, like the power of the stone all the time. That could make life a living nightmare.
So after thinking about it, Jon knew just what to do. That night, holding the stone, he said, "I wish that I, despite being a familiar and familiars generally having less magic than witches, would have ten times as much magical ability and talent as Zoe, and that anything further she tries to do to me, I will be aware of what she is trying to do, and it will be at my discretion if I allow it to happen."
There, that should be a minor change with no negative repercussions. If Zoe planned on treating him respectfully and this witch-familiar relationship she had in mind was going to be more of a partnership than it was for most of the familiars, she might never even know. But if the need arose, Jon could take the control of the situation, without relying on the stone being in his hand the moment he needed it.
