I dunno much tech-wise.., but just judging by what's done in 2142 (northern strike specifically), base it off of the goliath, with sub-structures that can be destroyed to reduce it's auto-repair ability.
In this case, the sheild generators being the weak spot, and the autorepair could just be very fast acting, to seem more like sheilds...
for sectional sheilds,look to the security doors in the titan... they are sheilds that are brought down one at a time...
so you make the sheild (which lets friendlies pass, but not enemies) stretch to cover one quarter of the ship... hopefully you can bend it like the main titan sheild... where i get stuck, is figuring a "console destroyed" effect for each sheild, be it a large ivisible overlay, or a not terribly lore-friendly ship protusian.
personally, i like the rogue squadron games where you just need to shoot the big sheild generator balls on top of the bridge before its sheilds go down.
the hard part I'd like to see done is sectional damage to capitol ships, where large chunks can be missing with fires coming out...
It's not Camping anymore, it's "Strategic Defense".
... I didn't ram you, i simply didn't care that you were in my way.