Many RTS games let you tell your production buildings where to automatically make the produced units travel to when they spawn. This is usually done per-building.

However, with battles fought on many fronts, you should be able to place global "rally points". Instead of setting locations per-building, you set multiple rally points and buildings (or spaceyards in your game) would send their produced units to the nearest rally point (even if it's across multiple parsecs of space). You should be able to manually override it for buildings, telling a specific building to send their units to a different rallypoint even if there are nearer ones, but in general as your "frontlines" of war move, you (the player) can just shift your various rally points around - say, a half dozen of them for different lines of war.

I generally like the idea of fleets being composed of ships in various states of advancement and various states of age and dilapidation. However, if it decreases the enjoyablillity in one area of the game (some ships slowing down entire fleets), work around that flaw to make the game enjoyable even if you have to do some handwaving (make entire fleets move at their combined averaged speed, or at 0.75 of the difference between the fastest and slowest ship).

Servent, one good example of this is the new Planetary Annihilation. The player can double click any structure(like mass selecting units) to select all alike structures (SCII does this as well if I'm not mistaken). Once the player has mass selected the production structures they can then not only select a group rally but create queued rally location and/or patrol areas for all units produced to move or attack-move to. Its a great system in real time and I can only imagine it would be useful for turn based as well.

As for unit speed, I've always thought it would be interesting to have variable control of unit speed using the mouse wheel (or something of the sort). It would be interesting to be able to push ships beyond their engines capability at the risk of a meltdown. The variable control of the mouse wheel could be case sensitive as well. Cursor over friendly ship to adjust shields, cursor over enemies to adjust power to weapons, group select and micro a squad of starfighters to "set shields double front" or "go in full throttle this time, that should help keep those fighters off our back", etc.

This topic made me realize it's the "thinking of individual ships" that I loathe.

How a "real" imperial campaign looks like. The Grand Admiral is sitting in front of a holo-something and sees the insignia of formations (in land military the smallest unit at this level is division) grouping tenths of thousands of ships, he/she does not see individual ships, actually, the high command doesn't even have access to that information! Line commanders DO NOT pass to the high command the information where each solder is or a platoon or a company. Actually, the high command does not even communicate with line commanders directly at all :)

And how it looks in games? You feel like a low level logistic officer that needs to act because the supply of toilet paper on some small frigate is running low...

I generally like the idea of fleets being composed of ships in various states of advancement and various states of age and dilapidation.

Yeah, I like it too for some reason. Some rusty outdated ships have an appeal of some sort I suppose :)

BTW: I propose to split the Speed of fleets discussion to there: http://www.gamedev.net/topic/658326-speed-of-fleets/ since it seems to be a bigger issue.