... If you want to be objective, how worried are you about maintenance? The S4R by its nature will require more involved maintenance than the S2R. If that's a big issue for you, then there's your answer, I guess.
Speaking of maintainance schedule, on the new 2007 bikes the intervals have changed from 6k to every 7.5k miles. Furthermore, the 6k service on the 2006 and older bikes require around 6 -7 hrs of shop time, the 2007 models only need 2.5 hrs. That's a huge savings on maintainance for the newer bikes and something else to consider.