Firstly, let me congratulate on a good idea for a mod and the original makers of the graphical design, solar system implementation. Love the chance of really getting to play MOO2Civ in the future.
I just had a thought about stealth. In Civ4 you have submarines and units that can see submarines. These are not the same as units that can see other stealth units, or are they?
If there are special cases where some unit can see certain units from stealth only, there's a chance to get more variation in stealth types.
On to the suggestions I had in mind... I do think you have also thought of most, just didn't find myself searching enough. I also don't have much modding experience, I've just toddled around the SDKs a bit, and have some experience in game programming so far
Exploration
Exploring is too easy, there needs to be a range limiter that doesn't allow venturing off too far, or the unit might never get back home. A problem with Civ4-mechanics ofc, but thinking of how aircrafts re-base, or do recons, there could be similar commands that included travel time or something. For starters, it could be just that the unit is unavailable for the duration of the journey taken.
Culture could be used as fuel range in a way, but wouldn't make use of extended fuel cells at all. Would also mean redesigning culture usage in the mod.
Ship desiging and refitting
I find the lack of ship designing disturbing. This is supposed to be a spiritual descendant to MOO2, and ship design was important in it. This is ofc countered somewhat with promotions, but the fact that units gain experience in combat and get new promotions from it feels wrong: you don't get mass drivers in a ship that just blew up some random ship in the middle of nowhere.
Maybe the ships would need to be launched from space dock in order to be usable, and they would lose experience points, and a promotion that would allow space dock upgrade promotions. Let me better explain what I had in mind:
A ship is built in a space dock. It is immobile and can not defend or attack, but it has a set number of experience points to be spent, and a promotion called "in space dock". This would give access to ship equipment promotions.
A player chooses what the unit has, and then activates a command that launches the ship from space dock, removes the experience points, resets the level, but keeps the given promotions as free promotions, removes "in space dock" promotion and adds a promotion named "launched" which would be required for any ship crew experience promotions etc.
Complex, but not too bad from a programmers perspective. Refitting should also be possible IMO, but I don't have many good ideas for that. Maybe something to exchange existing promotions to others with increasing cost to build or buy, while retaining the prerequisite hierarchy.
Hope my ranting helps