I thought that would be a big factor too. Virgin themselves (so lord knows it's got to be true!) stated that it can reach its maximum speed up to a minute faster than the current fleet. If you factor that in and think about all the times the train has to speed up and slow down over the course of a long journey (not just at stations but for other restrictions) and that will soon add up.
I've not travelled beyond Bristol on the GWR but using the ECML as an example, if a train is leaving London and stopping at Stevenage, Peterborough, Newark, Doncaster, Darlington, Durham, Newcastle, Alnmouth, Berwick, Dunbar and Edinburgh, it should save a significant chunk of time just on stopping and starting. Factor in the electric doors and the number of times it has to slow down for other things (Curvy track between Darlington and Durham) and it's easy to see how a journey could be made much shorter, even though the train isn't travelling any faster.
Does anyone have any info on the estimated new journey times with the new trains? Kings Cross to Newcastle stopping at York and Darlington, for example?