Article in today's Times sport section "Cycling records are tumbling - but can this era be trusted?" In summary largely yes; lighter riders, less body fat, tighter jerseys, lighter bikes, better gearing, better food, sleeker frames, far greater use of the hubs rather than drops, deeper wheels, thicker tyres, use of aerodynamic tools means riders today compared to the height of EPO use are saving a lot of wattage.
Jonathan Vaughter's is quoted "I can say very confidently that the peloton is infinitely cleaner than in the mid-90s and that it's also faster. Those things are not mutually exclusive. But if you're saying 'Oh, now it boils down to individual cases', that's much harder. And for me to whitewash that and say, 'Well, I'm not even going to look at that with a critical eye, because I just believe that the equipment and nutrition is so much better' - that's also not appropriate. Because, obviously, the history of the sport is what it is. And you can't just turn a blind eye."