Hello,
If you are going for an XR, which is a good choice in my opinion, I would highly recommend a 250. Devol makes lowering links for XR's, which brings about an inch off the seat height. Furthermore, if you decrease the shock preload it will also bring the seat down a bit.
He will very quickly outgrow the 200, especially with the lack of suspension on the newer model 200's. The 250's have much better suspension, and it's tons easier to get aftermarket goodies for the 250's and bigger. Both of you will be happier in the long run if you get a 250 over a 200.
I'm an XR freak, but I've heard great things about the new Yamaha TTR's. I believe, they even have electric start, but they are also a bit more expensive if I've heard correctly. Trying to kick start a bike you don't fit on is tough, so the elec. start might help him fit into a bigger, better bike.