Changes in the requirement: well, yes. They should stop doing that, it's really expensive if you start messing a contractor around after they've started work on something. This applies to everything from combat aircraft to wallpaper. The argument I would have with this is that trying to predict what's going to happen in the future has been shown (by the problems we're discussing) to be effectively impossible. So, don't try: instead, build something reasonably general-purpose. I saw an interview with someone involved with Tornado operations recently in which it was pointed out that the thing has never actually done what it was intended do - interdict the Warsaw Pact - but had been successful nevertheless. To some extent, yes, if all you have is a hammer everything looks like a nail, but at least make it a flexible hammer and don't keep messing the spec about.
Cost before risk: sorry, this is just balls. Heads the contractor wins, tails the taxpayer loses? That's exactly the sort of madness I'm talking about. I know BAE is effectively a monopoly, but that's what this thread is about. It's their problem to characterise the risks and contract accordingly. Deals where they make all the money but the taxpayer shoulders the risks are insane (and typical of PFI, and PFI-style contacts in general.)
But as I say, the argument is not only with the contractor. The argument is with the decision to omit catapults and arrestor gear from the carriers, making the air wing more expensive but much less effective. The argument is with ignoring engineering advice on Type 45. These are not normal contractual issues, if any of these are (they're not.) These are stupid decisions made by idiots and it is not okay.