Ohh this millennium.
I'd say, steady progress in direction of trials specific frames. Shorter chainstays, little higher bottom brackets, longer wheelbase and of course shorter seat tubes. Just look at the bikes from 2000 http://www.davedennis.freeservers.com/bikecandy.htm
That's for stock bikes, I've never rode mod but it's probably the same http://www.bikepedia.com/quickbike/BikeSpecs.aspx?year=2002&brand=Monty&model=219+X-Hydra
I don't think that progress in brakes was essential. Sure it's nice to have more stopping power, but even back in the 90s with proper technique brakes wasn't the limiting factor.
Modern freewheels are great too, no need to buy Chriss King hubs that costs arm and leg, or shittier Shimano silent clutch or generic ones which would explode every two months. Modern freewheels made trials more affordable, however it is more of convenience than progress in terms of pushing trials forward.