Hello,
Good question. Unfortunately, I have never ridden one of the new Yamaha thumpers. I've heard they rev alot higher than the XR's that I'm used to, and handle better than a stock XR.
Regardless, I think the weight, compression braking and the torque down low are the biggest differences. It's hard to explain "how" to ride thumpers, you kinda have to get some time on one and adapt your own techniques.
Because of the torque and lower instantaneous wheel speed, you will get more traction on a thumper. This makes it harder to steer with your rear end by lighting up the rear wheel. When you factor in the weight, thumpers aren't near as easy to throw around as a 2-stoke.
The smooth power delivery of thumpers requires a smooth riding style, in my opinion. Like a race car, smooth, fast lines through turns and hard controlled braking are key to being fast. Good luck.