In my experience, you have far less leverage as the buyer of a new motorcycle than you do as the buyer of a new car.
I wouldn't expect a break on any of the dealer fees, as it seems to be the case that all of the motorcycle dealers have decided to charge very similar fees to eliminate that profit center from their competitive exchange with one another.
Similarly, I wouldn't expect much of a break on current-year models either. Expect to pay at or above MSRP until there's a model year clearance sale.
Now, if you're willing to shop around and drive a little bit then you might be able to get a stupid good deal on a last year's model. I bought a brand new 2011 TW200 about 4 months ago for about $4K out the door. I had to drive a couple of hundred miles to get that deal, but when the best out-the-door price I could find locally was a USED 2011 TW for $5300 I felt like it was a steal.
Now this is all assuming that you're paying cash. If you're financing then you're going to get ripped off no matter what, but if you've got cash to put on the table then you should be able to find a deal on a leftover if you google Yamaha dealerships around your closest metro areas.