I'm so far in agreement with Taggerung. The rules so far in BFG:R are simply an evolution of the current rules that allows for mixed cap ship/escort squadrons and individual special orders. The proposals being thrown about here are a fundamental change, and I'd like to err on the side of caution for now.
There's only one ship I can think of at the moment that would really abuse the inability to target it directly, and that's the Avenger thanks to its strong linebreaking ability and lack of vulnerability from any other angle. Both the 5+ prow BBs are too slow/marginal as gunships to abuse it, the Vengeance/Exorcist are priced high enough for it not to matter, and the 5+ light cruisers are comparatively easy to attack from other angles.
Also,
@RCG
I think that the method you've described is at once too harsh (you get one straggler and the rest of the squadron is paralysed?) and convoluted (wait, what ships can go on what orders again?) and doesn't address the two biggest issues with capital ship squadrons: targeting and spill-over.
A line of five ships has the centre ship destroyed, dropping it out of formation in two groups. Define 'the rest of the squadron.' This is a significant difficulty in the official rules which effectively forces the penalty to apply to all ships.
I don't think it's convoluted at all. A ship can go on any orders it likes, but not two at once. This means that if any ship in the squadron is on orders, the squadron as a whole may not go on orders and vice versa.
