I agree with jwood. also, the main thing this kid needs to do is to get him to be more active. things to consider is his diet, see how much soda/candy/chips, etc. this kid is taking in. I've had clients who would drink a liter or 2 of soda a day!
I agree with compound movements, he can squat with just hit body weight. if he's having a hard time squatting have him do box squats. You can even add in box squat to shoulder press.
Here's a little plan to get ideas flowing. The more muscles you activate the more calories burned. Give him exercises that he will get "the biggest bang for his buck".
Plan: Coach him on the basic exercises:
Squats w. bodyweight: if he cant do full squats, let him work in the range that he is comfortable. He needs to work on his mobility. if he's not going ATG that's ok. Because that will give him a goal to work towards. you can also incorporate box squats, and making him focus on form (hips back, chest up, etc.)
DB Shoulder Press: you can combine the squats and shoulder press together as one exercises.
Push-ups: have him do push-ups on an incline so his feet are on the ground and his hands are on a high surface even if its a counter top. have him to full ROM.
Lunges: he can do lunges, but same with the squats, let him work in his comfortable range of motion.
basically, work on his mobility. see what he can do, and make him reach for goals. For example, for him doing push-ups on a counter top then moving to push-ups on a bench, then push-up on to the ground is progression. When there is a kid who is obese you don't want him to be discouraged when he perform certain movements the right way, let him work into it through progression.
sorry if this is all over the place, but just got back from a great workout and pretty drained..