In my opinions, Yamaha failed themselves in making and getting the best out of their 2005 R6. It's almost plain stupid with the money they are paying Rossi and the success they are having ....
Well, the development of the MotoGP bike takes up R&D. And Rossi's salary. So, if you don't need to redevelop, why? I think Yamaha still sells every R6 they make, and that's got to be the goal of every manufacturer.
The cost of changes needs to be amoritized over the life of the bike. Why break something that's pretty darn good. Yamaha really has done a very fine job of continually refining an existing format rather than trying to redevelop constantly.
Ducati has used that method with some great success. Good example...916, 996, 998. The 999 is a departure. Previously, 851, 888. Three foundations with refinements.
Suzuki GSXR600's. Hard to keep track...Lots of platforms. Often complete departures from one to the other. Meanwhile, the calipers, and brake pads, on the current R6 have been used on all R6's, the R1's previous to '04, I believe, and might even be the same ones used on the YZF's...
Doesn't really matter anyway. It's done.
As for undertail exhausts, Suzuki completely re did the GSXR1000 for 2005 after redoing it for 2003...and gave it a side mount exhaust again.