There are real differences such as what Graham and Mark refer to, but the differences are mostly in flavor and feel. The two bikes are as different in feel as a BMW car and a Lexus. But like the cars, both are so darned capable that it's up to the individual.
Feel free to declare a winner, when they are this close there will still be a lot of people who prefer the other great machine.
There is one aspect that I haven't seen people bring up and it has to do with all the accessories that make the machines fit us as individuals. I may have the Yamaha, but I sure do like that there are more accessories available at reduced cost on the used market for the Beemer. The GS has been around for a long time and I recently saw a $250 Craigslist sale of a set of stock side bags for a GS that only needed a lock set.
Super Tenere & WR250R, AMA, IBA