There is also another factor that is having an huge impact on cycling performances: power meters. Power meters help a lot on energy and fatigue management and also on training in a scientific way. In the 90s (the EPO era that you are referring), pros used only HR monitor, right now pros are using PM and a lot of other sensors to track every details of their body.
I am not saying that there is no doping, but reducing the improvements only to doping is a bit silly.