Ok just a couple of points...
The freight traffic has increased over the last year or so. Whilst this is good for the envuironment, since it's Class 66 diesel hauled they are slow to get moving and don't go much over 60 mph. (What happened to Class 86, etc. Electric loco haulage?) They should be restricted to moving at off peak times only - preferably during the night which would make better overall utilisation of the route.
The problem with freight is not getting up to speed but rather maintaning it. The average speed of a class 4 freight is alot higher than a class 1 passenger that stops at nearly every station but the freight still takes lower priority. Electric freight traction is still used on the GE but only by Freightliner on certain services, DBS nor GBRF have the resources or facilities to use electric locos. Even so, electric locos bring their own issues, these being the frequent engine swaps needed at Ipswich which uses more resources (time, train crew etc etc) and is more fallable to problems with the OHLE.
Most freight services along the GE are booked off peak or during the night, but during the night is where most of the engineering work takes places which limits capacity considerably.
It seems a computer program is running sticking to the order of services as per timetable without any flexibility
Rightly or wrongly that is exactly how the railway is operated, to a booked path and a booked timetable....it reduces all sorts of problems such as overall delay and stock or train crew displacement.