While I am not privy to their business arrangements with BMW...I can make a pretty good guess as to why they are on the 1200GSs instead of the 650s.
First and foremost, the 1200GS is their flagship adventure bike. This is where the sales (and thus, the money) are. At the local dealer (Iron Horse BMW), they sell 4 or 5 1200's for every 650. They sell so many 1200's that they keep a dozen of them in stock at any given time. The 650s only come in 2 or 3 times each year...and only 3 or 4 at a time.
Second, Charlie and Ewan using them gives BMW a massive amount of publicity. And why would they want to draw attention to a motorcycle that is out of production? (F650s are in their last year--they are being replaced with the G650 line up). While I agree that the trip would be easier on the F650s, it would not sell as well. With no drama, you have a boring trip (boring to watch). And remember, this is about money. They need to give BMW a return on their investment...without that, there would be no sponsers making the trip possible.
As for why BMW instead of, say, KTM? Well, you remember that they wanted to use KTM's for the Long way 'Round...but KTM backed out of the deal. BMW stepped in, and now they are reaping the rewards. It makes sense for Charlie and Ewan to stay with BMW from a business stand point. It probably only took one phone call to get BMW on board with them...which removes one large piece of the project from their plate, freeing them up for the other aspects of the trip. Sure, there are probably better bikes out there (for this trip), but again, it is not all about the trip, it is also about generating revenue, both now and in the future. One aspect of that is maintaining relationships with the sponsers, and that involves being loyal to them *when you believe in their products*. Charlie and Ewan certainly appear to believe in BMW.