My grandfather started a layout when I was still in the womb knowing I was on the way. There was no Thomas or anything "age appropriate," and 31 years later I am still passionate about the hobby. I gather from what my mom told me the other day that I grew into it walking around with him helping him-what little one can do for ones first 8 years-build to it over the years.
I have a 3 year old nephew that loves trains and Thomas, and I envision adding an HO scale Thomas to run on my future layout, rather than build a layout centered around Thomas. As for my daughters, I am going to have to figure that one out. He is not gifted, he actually has autism, but he does connect with trains and lately I have seen him with his toy Thomas railset at home learning how to re-rail and couple them by himself.
Further, stearsmania, do what you want after you do some research. As much as this will be for your son, you will soon find it is as much about you if not more. Your son will take more from your passion than he will if you dumb it down. DCC adds sounds and lights, kids tend to find that stuff enjoyable.
Justin