Sorry about your son's bike being stolen... I remember how I felt as a 12-year old kid when my first real bike (a used 10-speed Centaur Italian racer) was stolen.
If there's anything I recall about outfitting my kids with bikes, it was the rate at which my kids grew, and my overestimating what they look for in a bike. So two quick recommendations: Keep it cheap and simple (which doesn't necessarily mean junk), and size it for growth. Have you looked into 24"-wheeled mountain bikes? I've see a few on eBay that make me wish I still were 12 years old.