I'd like to see warheads be able to penetrate the shields if concentrated, but do little or no effect if spread out. Like this:

So basically the ship's covered by invisible shields shaped like the part of the surface they cover. Combined, they envelop the craft completely. They re-spawn upon destruction (with, say, 5-10% hit points) and you can only damage the portion of the ship they cover while they are gone.
If possible, it'd be awesome if the game could tie a system message to each shield's destruction, such as "ISD JUDICATOR: BSHIELD 50%" (B shield at 50% hit points) or "CRL LUSLA: DSHIELD DN" (D Shield down). The messages could be standardized, so that A-E shields, for example, always referred to dorsal shields and F-I Shields always referred to ventral shields. Also, you could make it a rule of thumb that the first letters referred to the after shields. So an Interdictor cruiser could have seven shields, three below, three above, and one for the bridge tower: A, B, C, F, G, H, and I.
Of course there's a problem with lag, but I think this method would work great. If the ship has an external shield generator, breaking through to it with weapons fire and destroying it would, if possible through coding, permanently kill off all the SP's.
Only problem is I don't know how it'd handle fighter taking off and landing. I suppose they'd have to be allowed to fly right through the shield.
I agree with Safe-Keeper about the vague warnings, over specific numbers. It's more realistic and just... "feels" better.
Especially if the dev's implement sub-systems that can destroyed. Imagine having to head home not because you're heavily damaged, but because your lasers can't be fired until you repair your fighter. Would be awesome.
"One of the bitches actually gave birth while she was attacking, and her puppies joined in on the carnage."
--the awesomeness that is Boatmurdered.