_argv's changes look pretty good to me. FreeSpace has been needing an accurate energy system for some time. As for turret line-of-fire checking, you could use one of DirectX's mesh functions, D3DXIntersectTri. It takes five pointers to D3DXVECTOR3 structs: three corners of a polygon, the shot origin, and the shot direction. It takes three pointers to FLOATs, which will contain the u and v barycentric coordinates and the distance from the origin of the intersection if it determines that the line intersects the triangle. The function's return is a simple boolean value. It's not particularly efficient (you'd have to cycle through all the triangles in the turret's cone of fire) and I dunno if DX8 included this function, but it's one way of determining if a turret has clear LoS. It'd be easier if you were using the D3DX Mesh extensions, coz then you could use D3DXIntersect which cycles through all the mesh faces for you.
I've implemented a few of _argv's FS improvements in my own game engine from the word 'Go', because they seemed somewhat obvious if I'm going for extreme physics realism. The damage system I'm using is simple though, and doesn't prevent little weapons from hurting capital ships because my game is based around space tech in the near future. What would a 20mm cannon do to a Space Shuttle? NASTY...
What would a 20mm cannon do to a heavily-armoured space-faring equivalent of a modern Destroyer? Not a great deal, but it would certainly hurt if it kept shooting for long enough.
The shield systems I'm using are singular shields, mainly because the ship-mod code takes up quite enough processing time already (what with all the accurate collision-detection and positioning) and hence I don't want to make things even worse by calculating exactly which part of a ship's shields got hit. Singular shields simplifies the FX stack, too. Instead, when a ship's shields are struck, they glow slightly. Normally, shields are visible as a specular reflection on a semitransparent globe around the ship.
Shields? In a near-future game? Yep. They're developed by the American forces first, and they only deflect energy weapons. Plasma 'ghosts' through them, dealing full damage to hull but depleting the shields too (VERY deadly weapon, the Plasma Accelerator Coil, aka PAC). Mass weapons ignore shields entirely. Missiles with RADAR-based tracking systems have a small amount of trouble locking on through shields.
If I EVER get my engine finished, I'll modify it for FreeSpace use. Same HUD, same (or better) AI, same ships, same shield hit effect types. But it'll be DX9-compliant, and I'll sure as hell figure out vertex and pixel shaders...