Is he wanting the bike, or are you wanting him to have it? Don't take that wrong, I'm just trying to make sure we're looking at the right thing.
I'm inclined to go with one of the #3 bikes, but then, how long before it's not enough bike and he wants it replaced or upgraded? So I'd say start used, not new, then sell it to somebody else for their starter bike. OTOH, there are some nice 500 twins out there that are great starters and might last him a longer time after he "grows up."
It also depends on what he wants to do. Does he want to go off-raod, or stay on the street and highway? When he rates his independance is he going to ride to school? Is it important to him what his buddies think of the bike, i.e. sissy lil' 250, why not get a real bike?
Great replies. Thank you.
A little more information...
I had limited motorcycle experience before I was 16 because my dad was a cop. Couldn't legally ride on the road, and dad wouldn't allow me to traverse any road to get to a riding spot. I had some fun on mini bikes at my Grandpa's farm, and had a moped when I was 15. The day I turned 16, I rode my Honda CB550four to high school. No real dirt experience for me, and the only time I have ever been hurt is riding off road before I was 15 (broken arm - hidden gopher hole, and sprained ankle as a passenger in sugar sand). Although, getting hurt on dirt and killed on pavement are two different things.
I loved that Honda. Probably too much bike for me, and only the Lord knows why I didn't die on that thing. Stupid things a teenager does on a motorcycle unsupervised while adding alcohol. My son is not like I was. Not even close. That's a good thing. Lost the Honda during college in a trailer accident (straps broke while on the trailer). Maybe a bigger reason why that happened. My wife rode with me on that bike, and enjoyed it. After we got married, I bought a Honda 650 nighthawk. Sold it a year later to help for the down payment on our first home. In 1993 I bought a brand new Vmax, but sold it in 1998. My son was 2 at the time, and I wasn't riding it. Couldn't take him, and couldn't leave him at home alone and take mom. So, in 2002 I got my pilot's license and bought a Cessna 150. For some reason, my son never really caught the bug on that. Still can't believe that, but when you're 6 to 12 years old, maybe you have other things on your mind. I sold the plane a little over two years ago because I was spending too much time and money on that, and not enough with him. Thus the "Pilot 2 Wheels" moniker. From a plane to two wheels.
I started looking at motorcycles again about a year ago. What I noticed, is that my son enjoyed looking with me. While out, he would always point out motorcycles, and ask about them. I could see the sparkle in his eyes. To confirm it, I gave him a copy of David Hough's Proficient Motorcycling to read. He also had to earn the money to pay for the MSF course. He did, and that proved to me that it was truly interested in this sport, and just not trying to make dad happy.
So, we have gone to many motorcycle shops and "tried" on bikes. So far, his favorite is the Yamaha FZ6R. Of course it is, he's 16 (almost). However, he likes the Ninja 250 and Honda CBR250 too, but what he also likes is the Kawasaki KLX. About the same as the Ninja and CBR. He likes the idea of going off road down forest roads and such. I like the idea of the adventure spirt more than I do the "GP" race spirit if that makes sense. I think the KLR would make more sense long term, but who cares about tomorrow if he gets hurt today. He is 5'10" and skinny. I'm 6'4", not as skinny. We can upgrade. I don't want money to even come close to a consideration over his safety. I won't let cheapness cloud my decision making. If I can't do it right, I won't do it.
He is a straight A student, top of his class. Smart like his mother (I know she is smart because she married me!

) His plans are to go to college, probably FSU (both my wife an I are alumni). A dual sport on a campus like FSU would be great to have. Parking sucks.
So, I am working with mom on a compromise. I think this is where I am leaning: First, he will take a minimum of 30 days driving his "cage", a 1997 Nissan Pathfinder. Mom's hand me down. Lucky kid. It's in great shape too with all the options and 4 wheel drive to boot. During this time, I have a friend who offered to let him borrow his Honda Rebel 250. He can ride that in the neighbor hood only. During this time, we will look for the right bike. If he wants to upgrade later, I may keep the bike if it's a dual sport, thus one reason I may go this route and buy it new, because I would probably keep it even after he took it to college. Used is probably a smarter choice though. I just don't want any mechanical problems to jeopardize his safety, and don't want to spend time and money fixing stuff. Time is precious, and I want to go riding when we can, not fixing a broken down bike. Another friend has a KLR, and will let me borrow it, so we could do a little dirt road riding. We ride together to these roads taking back roads. We do this after he has the car thing down, and spent some time riding 25 mph roads in the neighborhood. I know, the hood can be dangerous, but learning to start and stop, looking for cars backing out of driveways, kids playing, stuff like may help. I'll be with him when he does this to start.
My dad gave my one rule when I was 16. I had to ride 300 miles before I could take a passenger. Looking back, that was a little crazy. Times were different then. He won't take a passenger until I say so, and that will be me. I won't let him ride on his own for probably a year. More of a compromise for mom than anything.
Great advice, and no right or wrong answer. I try to be wise, and listen to all advice, but at the end of the day, it will be my decision. And yes, I don't want to mess this one up.
Keep any and all advice coming. I truly appreciate it.
Wayne