(I don't feel strongly about this personally, just listing some of the counterpoints)
Because the Rotary engines are something in between a 2-stroke and 4-stroke calculating it's displacement in comparison to 4-stroke engines was difficult.
For example, the trend of the past few years is to limit engine capacity and reduce fuel consumption. So the rules say your engine must go down from 3 liters to 2.4 liters capacity and now it's your job as an engineer to maintain the same horsepower (of roughly 800 hp) at that lower capacity.
Actually, changing those rules every year puts teams with lower budget at disadvantage: they are basically limited to buying engines from richer teams, because they wouldn't be able to keep up with all those rule changes on their own.
UCI has lots of rules around the size, geometry, and weight of equipment that can limit how much better you can make a bike. They even explicitly don't allow new innovations without their prior approval. Manufacturers find ways around the rules but to a large degree better bikes are actually not OK.