Lets try again.
One, whats the starting price point here? That does play into the picture... And competitive cyclist has 48cm S3's on closeout, is that where you're looking? $3500 or so for a 2009 S3 may seriously be worth it, unfortuantely, I squeeze myself onto a 54cm so I wasn't in the market...
Two, I don't necessarily see the changes to the S3 as minor. Shaping of the seatstays and fixing problems with internal routing, which can affect shifting, are pretty significant changes to a top of the line race bike. Easier to build, easier to service, and better shifting... To me, not insignificant when spending so much money. Plus, you're looking at a huge restriction on wheels, Shimano, Fulcrum, and Campy were basically all no go's, as well as some Mavics. This is pretty significant on a $4k+ frame as well...
Three, the 2011 R3 will be lighter. Period. Everyone's making the bikes lighter. There will be other changes, which you might find in other posts, and i've heard of several more. Just from weight standpoint, in being lighter, it will cut further into the aero advantage of the 2009 S3. If I were buying a bike that expensive (I have a 2010 R3), I would aim to have it for several years at least, even if you get a second bike for other duties. For me, if I were in your position, it would have to be a 2011 R3.
Thats my position on the question. The R3 is a fantastic ride and almost all the shop guys I know choose the R series over the S for their race bike...