J.D. is our narrator, and also Tom's younger brother. Looking up at Tom, J.D. admires him even as he questions his brother's motives. He wants to stop Tom, and he wants to be Tom. In other words, he's the Nick Carraway to Tom's Jay Gatsby. Doubt our literary leaping here? Consider this: The Great Gatsby, and The Great Brain are awfully similar titles.
Importantly, the subject of J.D.'s admiration can only be described in superlatives. Tom is great, while J.D. tags along, struggling to keep up. Because of this, one of J.D.'s more important roles in the book is as the little brother who reflects Tom's glory. You know how J.D. goes to great lengths to be the brother who gets the mumps first? In no time at all, Tom turns the tables on his younger bro, rewarding his ingenuity with the silent treatment and even finagling a belt out of the deal:
It was worth the belt just to have him talk to me and say good-night to me. Before going to sleep that night, I included Tom in my prayers and thanked God for giving me such a big-hearted and wonderful brother. (2.128)
J.D. says, "I took after Papa and had curly black hair and dark eyes" (1.7). Thing is, that's not the only way he takes after Papa—just as Papa is always taken in by advertisements for amazing new inventions, J.D. is always taken in by the Great Brain's amazing schemes. See the belt incident above. He might only be eight years old, but still; J.D.'s kind of a sucker.
As much as J.D. complains about Tom's constant scheming, he finds life after Tom's reform pretty dull. He's the perfect little brother figure: While Tom drives him crazy sometimes, he also worships the ground Tom walks on and loves watching his plans succeed even as he's jealous of all the attention Tom gets. J.D. would like to have it both ways—he wants the fun of Tom's hijinks without the potential for getting in trouble. We can't blame him. What is there to do in 1896 Adenville besides watch the shows Tom puts on?
One more thing we need to point out about J.D. is that, in addition to being the narrator, he's kind of a stand-in for the author of the book—you know, since J.D.'s full name is John D. Fitzgerald, just like the book's actual author, and he has an older brother named Tom, just like Fitzgerald did (source). Plus, though fiction, The Great Brain is set up to look like a memoir. Fingers crossed Fitzgerald never gave his siblings the mumps.