I really hate to predict it... but the R3 will be dead by the time they are done, and considering it's existence is only as a Halo product, and not as a leader in sales. I doubt, but hope, it gets an update rather than just killed off outright.
The bikes as great as they are, are incredibly behind the times. They were never diversified, as you mention, into a platform for a family of bikes, but left to rot with 3 versions of the same bike bearing different names and incredibly minor tweaks over he years + a tourerish version. I just can't see the company that outright killed the Daytona 955, then built a 1300 cc Daytona prototype capable of over 200mph, then killed the program and stated there will never be another big daytona again refreshing the R3.