The difference between XR650L and XR650R is huge. I rode a dual sport XR650R for years and loved every minute of it.
XR650L: The XR650L is more like a XR600. It has a round steel frame, air cooled, mild mannered and is based on late 80's technology. It's got to be the longest production run for any dual sport bike out there and there's a reason for it. They're great all around bikes.
Cons - Heavy, underpowered, heavy, weak subframe for loading gear.
Pros - Reliable, electric start, go anywhere, comes street legal.
XR650R: Built to win baja. All aluminum frame, liquid cooled, built to team honda specs. It's a race bike make no doubt about it. They make decent adventure bikes, but it's a thoroughbred vs. pack horse.
Cons - Heavy, kick start only, essentially no subframe for loading gear. Have to dual sport it for street use.
Pros - Reliable, go anwhere, lots of power
These are big bikes for tight trail riding. The R has a very high seat and some people under 6' or inseam challenged may find it difficult to get a leg down when needed. They're definitely called BRPs, Big Red Pigs, for a reason.
The plus is that they are extremely reliable. The maintenance intervals are manageable, and parts aren't crazy expensive. Also the dealer network for Honda is huge.
I loved mine in the open desert. There isn't another bike out there that performs as well as the XR650R in wide open runs. Huge amounts of torque, low end response, and point and shoot attitude. The same things that made it so good in the open made it a bit tough on tight single track. Once you get used to the bike it's not so bad, but it's also not a lightweight 400cc bike by any means.
The last year of the XR650R was 2008, so even the newest ones are five years old. Mine was a 2001 and was a former baja bike. It was used and abused, but still ran like a raped ape and needed only basic maintenance. They do eat tires up though due to their power and weight.
Check out ADVRider for a lot of information on these type of bikes.