You're exactly right. Here's the story. Way back in the mists of time, basically everything was four-stroke. These were the days when a stripped Harley was a competitive off-road machine, and the major games in town were the British thumpers, like Triumph, BSA, etc. Two-strokes weren't used much because their powerband was a little freaky and they didn't make very much power anyway. Then, along comes the expansion chamber, which transforms the two-stroke into a powerful, snarling beast. I've got a really old two-stroke at home that didn't come with an expansion chamber as we'd call it today, but after we put on a custom aftermarket pipe, it became a radical crazy machine of death.
Okay, so we have these powerful two-strokes hitting the scene, and to top it off they're also very light compared to these four-strokes, which were really just a stone's throw from being full-on street bike motors. Makes like Husqvarna, Bultaco, Maico, and CZ come in and dominate the four-strokes, and remember at this time the rules just said your displacement had to be X, without any distinction between the two. By 1974 or so, there wasn't really anyone seriously touting a four-stroke in motocross, and this was incidentally the greatest boom period for the sport. Everyone and their dog rode motorcycles.
Fas forward to some point (not exactly sure when) in the 1990s. By this time, the 500cc class, which was the most popular class until the day they ended it, was eliminated. The big names that had started the two-stroke revolution were almost all relegated to limited production runs and none could mean homologation requirements to race. A new rule hits the books to encourage more variety in development, because bike technology hadn't really gone much of anywhere in the previous ten years. Four-strokes would now be allowed to run at 550cc in the 250cc class! No one jumped on it at first, but eventually Yamaha made the YZ400F, stole the 250cc championship, and it was a media blitz from there.
Pretty soon, they cut the handicap down to 450cc, possibly because KTM made a 525 with some serious balls and it threatened to take over the world. Naturally, because the four-strokes were (and still are) twice as big, they've got more power (just) and have been making a clean sweep through victory lane for some time now. Whenever the thought of going back to equal-displacement comes up, the response is immediate and powerful from the major bike manufacturers, who sell almost nothing but four-strokes, and make a killing on parts and service when they inevitably go nuclear.
So, there you go. They certainly SHOULD compete on equal-displacement, because that encourages innovation and efficiency in design. But you know, politics.
