Hate to break it to you, but there are larger differences than 0.01%. Most are evolutionary, but all around you can find examples that are as close to revolutionary as any of the bikes you have mentioned. Look at the changes in weight, stock use of slipper clutches, radial brakes, Honda's change of rear suspension mounting location and now the upside down swingarm on the R1. That was a very obvious distinction on the R1, and if you missed it, then you aren't looking very close.
Other changes you might want to note include the frame going over the engine on both the ZX-10R and the new R1. Btw, have you heard any of the old racers mention that most of the Liter Class bikes are good enough off the show room floor to beat the best 500cc GP bikes from 7-10 years ago?
Also, Sport Rider did a comparison of a modified 2000 R1 against a 2003. If the new bike wasn't quite a bit better, the suspension and exhaust changes alone would have made the old bike considerably quicker than the 2003 on the track.
If you want more changes, search on roadracingworld.com for the patent given on the Tularis. It changes the direction of travel for the rear shock in a dramatic way. It will be interesting to see if any major manufacturers follow suit. I have seen this bike in person, but am sure many have not so I will explain a bit. The Tularis is a bike built similar to 500GP bikes, using a Polaris Snowmobile Engine. It is extremely lightweight, which allows it to develop a power to weight close to a liter class bike.
If you add all of this up, it shows there are more changes happening now than before (at least in my opinion), but they are being made by more manufacturers. When everyone works to improve their bike, the changes by any one manufacturer are not as noticeable.