Other options I'd want:

Fleet Tactics: You could tell your ship how you wanted it to determine which ship it attacked
Choices:
1) Worst- the easiest ship to kill
2) Best- the most dangerous shit in the fleet
3) Special- aim for special ships like transports or freighters

Also I'd create an escort module for ships, that would allow certain to override orders and take the attacks for bigger ships, so you could have a heavily shielded, lightly armed frigate defending the transports. Quicker ships would have a better chance of beating the escort however. I do not want tactical combat though.

Another thing I'd like- tractor beams, which would give a ship a chance to capture another ship. They could then either take the ship for themselves, or cannabilize the ship for money and research bonus.

I'd like to see Admirals as well once your logistics reaches a certain value, or with military academies. Admirals would work similar to the game Victoria- they would have traits that they could assign to a fleet/research ship/etc... Of course, the enemy could also bribe admirals should your approval rating or military strength become too low, or you could lose admirals randomly in combat/events. Admirals would only be good a certain number of years anyways 20-50. There would also be a limit on your admirals in that you couldn't have too many- a random "insubordination" rating would be given to each admiral, and your chief admiral could only have so many vice admirals, etc... Also, having too many admirals could lead to a military coup event, based on their traits and popularity- this could also cause your party to change.

I like the cloaking idea- at least in terms of sensor reduction.

I like the idea of a cloak-esque system, and it could be done without introducing any kind of fleet tactics. Introduce a "jamming" module which reduced the effectiveness of enemy sensors in detecting the fleet with the module. Sensor range could be reduced to 1 / (1 + N) where n is the number of jamming modules in the fleet, so 1 module would halve sensor range, 2 would reduce it to 1/3 and so on. This would pave the way for specialist jamming ships that could hide a fleet from detection at all but short ranges. If the above formula seems too harsh 2 / (2 + N) or 3 / (3 + N) could easily be used instead.

See my similar comments on a post I made about ship combat and retreat.

I feel that having tech that allows you to retreat from battles sort like way Civ IV does it would be nice and allow tech that reduces or elminates retreats options at the expense of combat or defense tonnage. IF retreat was added it should be very low chance something that rarely happens it would get very frustrating to fight the enemy every single time and have them escape every single time with their largest ships. Something on the order of a formula where the fleets is outgunned over 5 to 1 the computer makes a check to see if retreat is an option then a formula of say 2 percent for any remaing ships to retreat boosted by tech up to 10 percent but reduced by enemy counter mesures by up to 9 percent. Cloaking device would obviously add huge to retreat chances but this could be offset by enhanced scouts in the enemy fleet that have advanced sensors which would negate the cloaking affects or mitagate it to large degree. BTW this option would give more reason to build scout specific ships and provide huge reason for players to protect them since they give advance warning of fleet movements and negate any cloaking device and or retreat bonuses.

As for leaders I think the MOO2 Approach would be best IE You can have only a handful of fleet admirals, captains, planetary governors, or diplomats even. Since legendary leaders in history are some what rare they should be rare in game and cost economy upkeep to keep. Plus I feel they should increase in upkeep cost as well as they become more valuable. IF i were to suggest it they should be only 4 per race.
One advantage would be to have a legendary captain that gives a legendary retreat bonus (nothing huges say 20 percent retreat base plus tech) but restrict their deployment to cruiser size or smaller. No one wants to see that impossible dreadnought keep comming back and back again.

Another item I seen voiced and would like to see is space monsters that add depth to the game. Every sci fi book or movie just about has one at some point. Unlike the older games give the monster a secret weakness that can destroy it easier and make it tougher to kill if its weakness type isnt used. Example Terrion the Nebula cloud beast would be vulnerable to missles,as the detonations cause it to lose gas, but all but immune to Beam, and/or rail guns which have no affect.
Also if legendary officers and governors in game and the monster is way too tough to beat you can use a sacrifice option to save your civilzation. IE the officer or governor thats CLOSEST to the monster can be sacrificed to destroy itm and adding a cinema scene when this happens showing it would be really cool, but alot work and might best be saved for an expansion update.

When i say expansion update I am talking about a paid expansion of course to pay for the huge amount work it would require and every game company needs to keep the cash flow incomming for the next project.