The 2 up capabilities on the S3 (or lack thereof) are the one thing that has stopped me from getting a Speed Triple TBH.
My RS (half faired and clip ons) is great for 2 up and as already stated you hardly know that they are there. FWIW my wife is 47kg and 5'1" (read little)
I make changes in my riding style when carrying her but the performance and the characteristics aren't changed overall.
I think the pre 05 models had the pillion a little lower than on the current model.