There are some reports indicating that Yamaha will release a "naked" R3, currently referred to as the "MT-320", in 2016. Such a bike will probably make a more suitable base for cafe racer conversion.
http://indianautosblog.com/2015/07/yamaha-mt-03-yamaha-mt-320-leaked-183309
http://indianautosblog.com/2015/07/yamaha-mt-03-yamaha-mt-320-leaked-183309