The key is in intergrated transport policy as expoused the fomer DPM John Prescott, sadly other than eating (then barffing up meat pies) he did sod all.
Manchester and Birmingham have good rail links, but where its needed is LHR & LGW (Southampton is ok too) if LHR had a mainline in from the North then the like of bmi services to LBA & MME would be dead, very few people use these routes if going city to city.
If i were running LHR and pushing for a new runway i would push very hard for a mainline rail service into LHR and not just a branch line