I absolutely love the idea of having the computers on a ship be ACTUAL computers!
Do away with \"AMC computer\" and BB missile computer\" and just have a computer running the program \"AMC\" Power users would then configure, or even EDIT the program, to alter the way the guns fire (or the way the engines work, or the way x happens)
Have a computer be able to handle a single processing \"thread\" like engine management. Link the computer to the engines, and the ship core. Then, you could either add a second computer, to run the guns, (and have another person use it if necessary... like a normal weapons computer..) or add a processor expansion to your primary computer, to run two programs at once.
Fighters and other small craft would run everything off of the same computer block, while Capital ships would have multiple redundant controll subsystems, all tied into the core. I would personally favor a redstone-wire style linking block, but it\'s not a big deal. AI emulation would be another program running on the computer, able to call other programs, and be edited if necessary. ((missile mode, here I come!))
Wireless signals, linking two ships would be AWESOME! that way, if you have escort ships, you can send them signals, to attack, to guard, to dock, or to execute programs designed on your own vessel. If the enemy hacks your command/controll password, they can turn your ships against you. If the enemy jams your signals (and his own, by consequence) you can not issue your escort ships orders. I would reccommend ALL player communication be done through a computer, with the proviso that there be an in-sector \"say\" style channel, un-blockable that would go through a player\'s suit.
DIsk drives = yes!