The "S" model is just the regular model with some cosmetic changes. Mechanically they are the same. If you don't like the low windshield the standard one will bolt right on or you can replace it with an aftermarket one. I have a Clearview windshield mounted on my 06 "S" model.
Things I like about the "S" model over the regular model are the absence of plastic covers on the handle bars and the extra LED brake light mounted in the spoiler on the back. If your plans include mounting a top case on the bike be aware that spoiler means the top case mounting bracket for the regular 400 will not work. I'm told Givi does make a mounting bracket that will work with it.
I am sure that it is all preference but when I went hunting for my Burgman I had the choice of the regular or the S. I liked the style of the regular one and the fact that it had a back support for the passenger. My wife sometimes rides 2 up with me and likes the back rest on longer rides. The back rest also comes in handy for carrying things. I can tie packages to the backrest if I don't have my tail box on. Today I bought a milk crate from Walmart for those occasions so that may change. Before this I would carry a gas can back there when we would ride any distance because her scooter only has a 1.4 gallon tank.
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