Just gave this thread a bit of a glance over and feel I need to make a point about not making the game *too* hardcore. You still want a large enough population to keep the game going so you're going to need to make it accessible enough to the average rts gamer. Theres also the problem with tactical variety since with such a high degree of micro people who want to play something fast will be punished more than those who play slow lumbering ships, even pro gamers will be encouraged to play slow ships since it'll give them an edge. I'll probably touch on this in more depth later on...
A good way to look at this is that you're not piloting each and every ship (who could?), you're commanding those who are... each ship has someone inside them with the sense not to shoot at or collide with friendlies.