The short answer is that the CAA simply will not allow Lightnings to be flown. It's easy to get wrapped-up in all the technical babble about complex catergories, design authority issues and all the rest of it, but ultimately it's a simple issue. The CAA take the view that the Lightning isn't safe enough, even though the aircraft would receive more direct and intensive attention than they ever did whilst in RAF service, and yet the MoD judged the aircraft perfectly safe to fly in UK air space for decades - but now they're not...
If you look at it like that, you can see why I (and lots of others) think the CAA's attitude is ridiculous. The CAA is very good at wrapping things up in technical jargon and red tape but ultimately it's simply down to their judgement and I think their judgement is flawed. Likewise, I'd love to know how bodies such as the CAA are allowed to sit in judgement on such issues while we citizens and taxpayers have no right to question them or appeal against their jumbled logic.
But that's the way it is I'm afraid. Some "expert" decides he knows best and we're stuck with it. Of course there is no logic to the notion that a Lightning is somehow more dangerous than your average Cessna. They'd both ruin your day if they landed on your roof and yet, when you work out the odds of both types of aircraft ever actually causing any such damage, you realise that it's absurd to imagine that one or two airworthy Lightnings would be any more of a risk to our lives than having a road going past your front door.
But then, that's our Nanny State for ya!