2 sides to the problem
Firstly a confession - I worked, as an employee for a company supplying equipment to the MRA4 flight simulators - yes, there was a very nice building at Kinloss fully populated with 2 full-flight sims (motion sims for the cockpit), 2 FTD cockpit simulators (same as full-flights without the motion) and 2 rear-crew simulators and a bunch of PTT and other kit. These were all accepted and in full service at the time of program cancellation. All are now scrapped.
The problem was two-sided.
1) The MOD was unable to write a spec worth a bean. You might as well said we need some simulators to train the crew, once you've built them we'll tell you what is or isn't any good.
2) The contractors (everyone from BAE down) were desperate to win the contracts, so promised the moon... for next to a penny. And then charged whatever enormous number they could for any change order the MOD was backed into a corner to put in writing.
As far as we (the engineering team involved in developing the sims) could tell the entire program was run the same way.
At the time of cancellation I was personally involved in a quotation to update a part of these same simulators that had seen only acceptance crew through the doors, to the tune of $1-2M for a system that had only been operational for 3 years and was ALREADY obsolete. This update would have replaced the original system with something costing twice as much, to do the same job. This is a very tiny slice of the what was happening across the board.
-GY