Decades prior to that, several decades, in fact, motorcycles with intakes at the front and vice-versa were not that uncommon. The exhaust forward set up became common practice for several practical reasons, just as the majority of large displacement V-Twins have heads "reversed" and cylinders angled back. Yamaha here has reversed the head from what has now become standard for other practical reasons. Since EFI is reasonably commonplace, and perimeter frames were nothing new when Cannondale used one, the only particular design element unique to the Cannondale that the YZ uses is the reversed head. Hardly makes it a copy of any kind, especially considering that they are otherwise so different.
When Yamaha came out with the original 4-stroke MX bike, that was revolutionary. Cannondale took that concept and added tunable fuel injection, aluminum perimeter frame, and a rearward facing exhaust port. And they did it several years ago.
Your point as to evolution vs. revolution is spot on. The Cannondale was a mutant that died out for a lot of very good reasons, none of them having to do with where the exhaust port was. The YZ400 has been revolutionary.
You are slightly flawed my friend, 4 stroke motocross bikes had been around for years.... not as good, but they were there... so let's say this , the 4 stroke motocross bike from Yamaha, the YZ400, was Evolutionary, when the sport changed bc of it, it became revolutionary...
But it's well to recall that if you go far enough back in history, four-strokes dominated MX and every other form of MC competition until the mid 1960's, when two-strokes that were both reliable and powerful enough to compete finally emerged. You say four-strokes were not as good in those days, nothing was. Two-strokes of the 1950's were hopelessly unreliable, and not particularly fast, either. By the early 1970's the advantage of the modern two-stroke was great enough to have taken over MX almost completely, leaving the world as it was up to 1997.