Excellent tale, and well-told to boot. I enjoyed Jon's journey from surprise ("I can hear people thinking! Hear them thinking? Yikes!") to agony of waiting for his father blended in with his fear that he's going a little nuts. The reunion scene was outstanding, and staying in Jon's POV with his actions and reactions in the forefront was excellent.
You do indeed have more to write in this universe. You need to answer some questions, explore Raegan and her family situation, and now Clark has to teach Jon how not to listen to his father and mother behind closed doors. I know the assumption is that it will be a fiercely passionate reunion, but there are several things they must deal with first.
Like - how long has Jon been hearing thoughts (great insight to have Martha understand first), why was Clark gone so long, what was the outcome of his time on New Krypton, does he have another family back there, are there any lingering obligations for him on New Krypton, just how much bitterness does Lois have saved up over his years-long absence, how long will it take each of the family members to adjust to the new reality of Clark being home, how much impact has Clark's experience had on him (both positive and negative), are his powers back (you hinted that they are or will be), will he take up the Cape again, what will he do for a living now, how much guilt will Clark carry for his long absence and his neglect of his parents and his son, just how bad is Jonathan's heart - the loose ends are almost limitless and rich with both dramatic and romantic potential.
Were I a gambling man, I'd bet - with a high degree of confidence - that you can handle all those questions and more with skill and deftness. I look forward to your next offering.
