As a regular user of the London-Edinburgh train over the past 9 years, my observation is that it depended on whether you are on a through train or not. If you were on the Aberdeen train than it tended to stop at platform 19, so the 1st class carriages would be closest to the centre of the station. Otherwise the train normally terminated at platform 2 where the first class carriages were at the end of the platform and furthest away from the centre of the station.
The increased use of the old suburban platforms (on the Market Street side of the station) predated the change to Virgin, so I don't think you can blame them for that.
Roddy