More late night brainstorming:
Tactical combat. Obviously at some point our warships are going to have to wage war, and rightfully so. The xenophobic tholians have a right to defend there territory, and the klingons need to expand to survive. There are basically 4 ways to go with it, I feel.
1) 2D and realtime. Basically like playing SFC now, only on a larger scale (more ships, sometimes)
2) 2D and turn-based. Think like masters of Orion's combat system
3) 3D and realtime. I think this is my favorite idea. I know it deviates from SFB rules, but oh well. Essentially, it would feel like Homeworld.
4) Pure number calculations, like Civilization. (I think its boring that way, but it would be handy in certain situations. For example: if both players agree, the combat could be resolved like this.)
there ought to be an AI override on this, as well, methinks. If a turn is 48-hours, and a battle is to occur in that turn, you either have to fight your opponent, or you can have the AI engine handle the detailed battle.
In the cases of realtime, there should be flexibility in how you control your vessels - sort of like an AI autonomy setting (though, it'd be more complex than just a slider). Essentially you can select a craft, give it waypoints to follow (and even set the orientation of the vessel; maybe you want it to roll on its side to expose its dorsal shield; but thats in the 3D case) or tell it to attack a target, or harass a target, or even assault a target (use only phasers, stay at a maximum distance but still open fire, or attack with everything you've got, respectively).
Furthermore, you can set attitudes of any vessel you select under your command. The attitude would impact how the AI behaves, as well as energy priorities. Values could range from Aggressive (power to weapons) to Defensive (power to shields) to Evasive (power to engines), and so on. There could even be degrees of those attitudes: very aggressive (divert a whole bunch of power to weapons) or just aggressive (divert some power to weapons).
On top of that you should also have the ability to have any ship under your command perform specific commands, ie: launch a scatterpack, or fire a probe, or put this specific drone in your ammo rack and fire it when I say so, or grab a target ship in a strength:5 tractor beam, etc, etc.
I'm trying to plan for some pretty intense flexibility, here, allowing you to either sit back and watch a battle (but why would you want to) only give overall commands, or get into the heap and micromanage your ships, but only to the degree you want to.
On the strategic side.
I'm thinking a detailed economic system with trade (which is affected by relations between two members, ie: if they have a trade treaty, or are just on good terms).
A diplomatic system, which would only really be handy for treaties between live players, or affecting how the different AI players think of you.
I would LOVE to see things like morale for each unit/planet. If morale gets too bad you have uprisings which affect how effective the unit is. If it gets to a certain point, the unit becomes basically unusable. If it gets really bad there is a chance that the unit will either defect to an opposing player, or declare independence/go rouge. If the unrest is locallized but severe, there is a chance that the computer will spawn a new AI player for a new affiliation, or allow a new player to come on to control it, maybe. maybe like the LDR or Maquis.
In addition to diplomacy, there is espionage: steal research from a player, or find out whats going on behind his lines, etc. Careful, there is always a chance that you'll get caught - which could severely damage any relations you might have.
Characters should play a part as well. Characters are "recruited" or "trained" at certain facilities (Starfleet Academy). They have certain skill sets, and if they are assigned to a unit, they improve the effectiveness of that unit (or even a fleet, if they have achieved the rank of admiral). Characters can also be autonomous, and perform espionage or diplomatic missions. Hell, a character can even be assigned to a research facility, decreasing the time/cost of a certain research item (imagine scotty heading the development of a new warp drive system).
I'm not sure about the details of the economic model quite yet. I don't know much about real-life economics, so any model I come up with would likely be inaccurate. I know that there should be a few different resources: Metal, Credits, Luxuries, Research, Intelligence, and Food.
Metal and credits allow construction. Credits are also the medium for trade - buy X metal for Y credits, then sell Z research for W credits. Research items cost research points. Luxuries serve to "buy" morale - if a system is unhappy, ship a bunch of luxuries over there and watch your morale climb. Intelligence is the resource you pay when going under an espionage mission. Stealing a piece of research from someone is going to cost you in Intelligence. Food serves as an upkeep - the more planets you have, the more food you're going to need to supply them.