The plane v train argument has largely been settled in England - if I can get from Manchester to London, city centre to city centre, in two hours the train wins. I used to get the plane to Bristol occasionally, until I got held up in a traffic jam and almost missed the plane home (caused by a broken-down First Bus - were they in collusion?), but the journey has since speeded up and Air South West have gone out of business.
The Anglo-Scottish journeys are marginal - a lot depends upon where you are travelling to and from in each city, how much luggage you have and how flexible you need to be.
Once the plane is in the air its disadvantages lessen and you wonder why you can go to Prague or Tallinn for less than Edinburgh or Aberdeen.
I do NOT hope that the Air Passenger Duty is increased as this is a blatant rip-off, much the same as Penalty Fares, ever-expanding peak periods (Virgin), and ludicrous Anytime fares. I do use the train wherever possible, but if a carrier could wreck Virgin's, or any other TOCs, pricing policy by running ten aircraft from Manchester to London City every morning for £50 a throw - or they were forced to cede peak slots to another TOC who could charge the same for a couple of trains - I'd be very glad. My company will no longer tolerate this fraud and neither should the genral public or the rail regulators.