In the club that I race in, there is no "production" class for the street based two strokes. We are forced to run in a Superbike class, or a formula class. Since these rules are less restrictive then a production class, I can't really give you information on how the NSR compares to the Aprilia in a production class.
However, I can tell you that in the SB class, they can run very close times with riders that are equally matched.
Since the RS is a slightly newer design, it does have the advantage of suspension, and brake technology, but that can be taken care of by switching the NSR's suspension, and brakes with a Honda RS250 setup.
Power is about the same, depending on the level of tune the rider is willing to put into the bike.
If your looking for an all out winner, and your club has rules that allow for it, you should go with the Yamaha TZR, with a TZ power plant. Since the engine cases on these two bikes are nearly the same, the rules get a little grey, and people end up dropping TZ engines into their TZR's. This gives a power advantage of 15-20 more HP's. This will take care of anything that the TZR may be lacking over the NSR.
Also, the RGV can be made to run some quick times. There is an RGV in the club I race with that is looking to give the top runner TZR's a run for their money this year. Should be interesting to see how the RGV does.
Thanks,
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Charles Gallant