Of course you’re not the only one, nor should you pretend to yourself your feelings don’t exist. But how you choose to deal with those feelings directly affects his behavior, creating an unending cycle.
It worries me that you haven’t taken this into account. He could be depressed, anxious, angry or suffering in any number of ways that your favoritism is making worse. You should be looking for solutions – searching for common interests, taking him alone on a trip, therapy for him, therapy for you – rather than seeing this as a static situation (which no 12-year-old’s life ever is).
You’re his parent, and you owe him the hard work. No, you’re not required to like him all the time. But you are required to use your love to try to raise the healthiest and most productive son you can. He’ll be far more likable that way.
The biggest question here, to me, is not about the discrepancy between you two in terms of knowledge. It’s about the discrepancy in terms of curiosity. Intelligence doesn’t just involve amassing a long list of books read and museums visited.
We all know the undereducated genius and the overeducated paragon of cluelessness: Which one would you rather date? Does your girlfriend show motivation to figure out how things work, how aspects of the world are connected and how the past affects our future? When you make a reference she doesn’t get, is she interested in learning about it? Or does she look at her manicure and change the subject?
The former I could see having a chance. The latter? You’re smart enough to figure it out.