After thinking for a while Jon decided to change things, starting with his family.
To be honest, he mostly wanted to improve their overall life and his relationship with each family members. Jon figured he might as well start with his parents. He takes the wishing stone and holds it in his hand, thinking hard and carefully how exactly to form the wishes. After the minute he starts his first wish:
"I wish my father and mother were supportive, attentive and kind towards me, my sister and my brother, would be always willing to help us if we ask for advice or something, but wouldn't push too much into our personal lives." he pauses there and blinks slightly as stone glows and grants his first wish.
"I wish that both my father and mother would have very well-paid jobs that they both would enjoy very much, but would also pay attention to rest of the family and wouldn't be workaholics." he says his second wish and blinks at already familiar sensation of stone granting his wish.
While the first wish didn't really had noticeable changes, the second wish definitely changed things. For one - his room was quite larger. All of his belongings seemed to be of higher quality brands them before and he even had a large smart TV with his own gaming console and dozens of new games and movies. His bed was also larger and more comfortable. Overall, the house itself seemed to be never, or maybe it was just renovated not long ago... He couldn't really tell the difference.
Jon figured that seeing what exactly changed could wait until morning, for now he had a few more wishes to make.
"I wish that my sister Zoe wasn't a goth. I wish that my sister would be friendly, kind, supportive and trusting towards me and wouldn't do anything to harm me or our family." he says two more wishes, again triggering stone's glow.
He thought for the moment what to change about Jacob and decided to not do much "I wish that Jacob would be friendly and kind towards whole family and would want to spend time together when we can, but would understand and accept it when we don't want to spend time with him if we are busy or tired from something."
Jon looks at the stone after it finishes glowing and tries to decide if to wish anything else now or go to sleep.