The S50 and M50 are radically different bikes, with different frames, engines, drive lines- basically different everything. The S50 is faster, lighter, and about $500 cheaper, but the M50 has more contemporary styling, is roomier, and has a smoother ride. Most people are drawn to one or the other.
As for price, small motorcycles are getting more and more popular with high gas prices, the dollar is weak compared to the yen, and the profit margin on small bikes is not as fat as on a large bike. So you are not going to get a steal of a deal on an 800cc model right now. A 'good' price is MSRP + tax + tag fee + title fee. Anything below that, or any extra goodies they give you like a helmet or jacket, are gravy and make the deal better, so your best be is to shop several dealers and see who gives you the most free stuff with the purchase or who gives you the best interest rate on the loan, if applicable. You should not pay extra for assembly or dealer prep, as those are both included in MSRP.