Sentry does that, true, but I think we would all benefit from a "guard" function similar to sentry in that it ignores (or even user defined) things like enemy, low fuel, damage.
I think it would also help from a micromanagement standpoint if there was someway to order a ship to refuel as neccessary as it travels to a set destination. Doing the waypoint dance can be aggrivating. Something as simple as "when ship has half fuel, refuel at nearest resupply base on the way to final destination". I want to conquer the universe, smight my enemies, burn their planets- not play traffic cop.
Since the combat is going to be more or less real time, I might suggest that self-destruct components be given a moddable failure rate. Sometimes the captian isn't quick enough on the button, and this would add a little more variety to the current situation. "If I try to board, I will lose this ship- as opposed to... maybe, maybe not"
It might also open up interesting possibilites where certain components can be given "if destroyed, ship explodes". Hello engineering warp core! Maybe that uber weapon would have a certain drawback... or, another way to balance out the religious shrine (the staff on board, saddened at the defilement of their holy ship shrine all commit suicide to appease their pagan god) You get the idea.
I think a resuplly capability for a starbase (similar to the ship yard) would be a good addition. This would go a long way towards solving the resupply issues because of routing (assuming that a routing routine as expressed above could not be met). Make it big, make it exspensive, but damn it, make it so we can resupply (via a base only component) at a starbase on a warppoint!
This was touched on above, but how about happy modifiers with the use of certain stellar manipulations or types of weapons. You use certain devices (destroy a sun for example) and it makes your peaceful people rather unhappy. Bloodthirsty of course revel in it. Whatever.
Perhaps this is one for the modders, and not a stock game option, but how about the ability to research alien tech- the catch is that you do so at an extreme disadvantage (thing multipliers of 10 or 100) and the end product is never as good as a race who has a natural affinity for the alien tech. So temporal space yards would produce less for a non-native temporal race (but they could research it!) compared to a native temporal race. You could over course mod certain things as unattainble even then (such as the religious shrine) but damn it, why can't I grow organic armor!? I got a vat, I got the research! Gimmie.
