The Yamaha R6S is perhaps the most misunderstood of all Yamaha’s motorcycles.
The R6S designation (versus the usual R6) has some imagining that the letter S stands for sport, while others call the 6S a budget version of the R6.
So, what is the truth? The R6S designation actually originates from the 2004 YRZF6S code for that year’s R6. Yamaha decided to continue to produce the 2004 R6 model after the 2005 year, from 2006-9, as well as continuing to produce the evolving R6 model from 205-2020. The 6S code was retained for the 2005-9 R6S models to differentiate the two R6s. So every R6S is simply a newer held-over 2004 model, with only a few changes.
The regular R6 started going through changes beginning in 2005 in order to improve performance above 130 mph on the track, including modified brakes, forks, exhaust, etc., so the R6 could continue to dominate in races.
So, why continue making the old 2004 version if the new R6 was better? The 2003-4 model was already a perfected race bike and a wonderful and popular street sport bike. Changing the R6 for more top end performance also sacrificed some of the features Yamaha liked in the bike, such as ultra light weight, performance up to 130 mph, and street manners. Inverted forks are vulnerable to road damage, stiffer shocks are less comfortable, and the R6S is a faster bike on the street, where it counts for most riders. In fact, an R6S will easily out-perform a newer R6 up to 130 mph. Many people prefer direct throttle to drive by wire, and the bike was offered at a lower price as the research and development was already done and some parts were less costly (the older integrated exhaust system is half the cost).
The R6S did receive the newer frame of the R6, but was an unusual example of a manufacturer reviving a prior model and extending its production for many years. It demonstrates the confidence Yamaha of its 2003-4 R6 model.