Wall of Text Warning
Reading through this forum, Kryo stated that targetted (spellcheck?) subsystems as a concept was rejected as it would cause too much micromanagement. In my, granted quite limited, experience, it adds a great deal to the game.
For example, Homeworld 2, one of my favourite RTS games. A pair of Battleships warping in front of your mothership and starting to carve the hull apart is bad enough. When each disgorges a vast number of Bombers which systematically annihilate Engines, Fire control Centres and Manufacturing plants in the mean time, the concept moves from a survivable skirmish to one of those circumstances where only '... oh bugger' is really appropriate.
Further, one of the mods for Supcom is a modular damage system. This is a great thing. Few things are more amusing that carving the arms off an attacking force and watching the chatlog light up as the enemy commander rages at you. Micromanagement heavy, perhaps. Rewarding and deeply satisfying, unequivocably.
Fallout 3, I believe, is intended to have a 'modular' targetting system in a similar vein to those stated, which looks very amusing. 'Look, your arms off!' 'No it isn't.' 'What's that then?' springs to mind. If someone was/is working on this mod, or will be, please don't drop it. It'll be a good thing, and players will love you for it. I'm not great but I can model basic-ish things in max and maya, if you need such things done, and i offer my services as such.
much love