I've got a few ideas for what I'd like to see in a Tactical Combat System.
For starters, there should be 3 modes to handle space combat.
1- Control Battle (You control your fleets)
2- View Battle (AI controls your fleets)
3- Simulate Battle (CPU runs the battle very quickly and determines the outcome without viewing the combat)
As for combat itself. I think ships should always be grouped into fleets before launching them into space (much like MOO-3). Note that you could have a fleet with only a single ship in it if you wanted. The maximum number of ships allowed in a fleet should range from maybe 5 to 20 ships (higher level techs allowing more ships per fleet as you advance).
Multiple fleets will be able to enter the same battle (with perhaps a limit on the number of fleets per battle to keep things from bogging down). In combat each fleet is controlled like a single unit, with every ship in a fleet executing the same commands. So say for example you have 10 fleets with 20 ships apiece, you'd only have to control 10-units, not 200-units so it wouldn't be micro-intensive.
Each fleet would also have it's own 'Tactics Configuration' which you could setup when the fleet is launched (so the Battle AI knows basically what you want this fleet to do, without having to set it up for each combat). These Tactics Configs would also be used in player controlled combat to 'run' any fleets that the player hasn't issued direct commands for (say your fleet blows up it's target(s), it would run these tactics until you gave it new orders manually). Note that these settings would be changeable on the fly in battle too (you'd click on a fleet and have a 'Tactics' panel you could open to change things).
Tactic Setting #1 - Movement: This would control how the Battle AI moves the fleet. Here are some example settings.
Long Range Standoff: The fleet will attempt to keep targets just inside it's maximum missile range, and will not chase fleeing targets. If enemies attempt to pursue the fleet, it will attempt to move itself away while still being able to fire missiles on it's target. Good for carrier fleets, and fleets of missile ships with very little defensive weaponry.
Gun Range Standoff: The fleet attempts to stay just within range to use it's main guns on it's target, and again will not chase fleeing targets. It will also try to move away from enemy fleets that try to pursue it.
Short Range Pursuit: The fleet attempts to stay very close and circle it's target, and will pursue a fleeing enemy. Good if you have a fleet of small fast ships that can stay outside the firing arc of a larger vessels main guns by circling it at close range.
Gun Range Pursuit: The fleet will attempt to pursue it's target, but stay just inside it's main gun range (as opposed to getting up close and personal).
Tactic Setting #2 - Target Priority: This controls how the Battle AI would prioritize enemy targets.
Capital Ships: The fleet will try to engage large enemy ships.
Planetary Defenses: The fleet will attempt to engage defenses on enemy planets (like MOO style missile bases, ground batteries, etc).
Interception: The fleet will try to focus on smaller enemy fleets, as well as intercepting missiles/fighters/bombers targetting other friendly fleets.
Tactic Setting #3 - Fighter Mission: This controls the behaviour of fighters launched from any carriers in this fleet.
Close Range Escort: Fighters stay close by the fleet and engage anything that threatens it.
Attack Fleet Target: Fighters will fly off to engage the fleets current target (but will still attempt to intercept enemy fighters and missiles while en route).
Escort Bombers: The fighters will attempt to escort any bombers launched from their fleet. (If all the bombers get destroyed, the fighters will behave like they do in Close Range Escort)
Tactic Setting #4 - Bomber Mission: This controls the behaviour of bombers launched from carriers in this fleet.
Attack Fleet Target: Same as above.
Attack Capital Ships: Same as above.
Attack Planetary Defenses: Same as above.
I think these "Tactics Configurations' would go a long way to simplify the space combat enough that it's not boring in the late game (like with MOO-2), but also allow players full control.