Well I think here's are a few ideas hat I would like to say
Ground Combat specific:
Possibly instead of just everything resolving in one battle I would wonder if the following system be implemented
When the invasion starts the land is divided into two parts, invaders and defenders, and per each week the number is rolled and for a certain amount of time battle is resolved (bonuses from the starting invasion will probably be negated following the subsequent rounds), depending on how the battle the territory changes and victory could be as followed
-When either army has gained the great majority of the land
-When either army has been exhausted
Also there could be the possibilities of allies sending in their own troops as reinforcements or enforcing your own troops with your own reinforcements.
The options that you choose before an invasion could instead be modules outfitted into the transport itself, also some penalties or advantages should be reduced if you use a tactic that the defender also has researched.
I think that during battle if the forces receive a significant loss of troops in one fight that some of the troops should have a chance to chicken out and flee the scene (reducing the army even more), possibly the Courage bonus could be used to prevent that and also to inspire the troops when it seems bleak to never give up without a fight. Also possibly a new tactic that could unnerve the enemy soilders and make them more likely to flee.
Make espionage able to gain a soildering bonus against the opposing forces since you possibly investigate force tactics, weapons and weaknesses (wait so coconut creme pies are actually very deadly against the Drengin)
Possibly in a lucky break one of the forces discovers some super weapon capable of annihilating the entire enemy force in one swoop (or if they don't know how to use it, they blow up on themselves and the defending force has a sweet little weapon to even the odds that could take an unused tile on the map... hey it happens in RPGs,) or they could wake up some powerful entities that annihilates both forces and takes the planet for itself (possibly with the +1% to stats per week thing too)
Maybe make PQ 0 planets something more than just space takers (I don't say that they should all serve a purpose and yes some should just be there to take up space but I believe there could be some use to them, possibly blow them up to reveal a resource or investigate certain planets to uncover bonuses)
Possibly certain tiles that could grant something if a certain biulding is put into it (specialized buildings of course, like lets say a digging site could uncover a bonus to social production to all your empire as long as you keep said biulding on it)
Repair bays sounds lovely
I really also feel that trading should not only be an economic boost to both and as a way to get the civs to be sweet with you but they could also impose a certain modifier to be more susceptible to your influence and be more willing to culture flip if it comes to that
A few new megaevents, here's a few that I would like to say
A certain civ has uncovered a capsule that contains an encrypted message from beyond this dimension, if the civ spends research time on the message they could immediately catapult themselves to a Tech Victory quicker than normal and without the prerequisite techs. Espionage could catch the message and prevent it from being ever found out... or they could relay the message to you. (Kinda reminds me on how the Tech Victory was won in GalCiv1 since part of it was that you found a message)
A huge explosion of popularity washes over the stuff brought from a certain civ and everyone is pawning their vital organs and souls to get it. Trade revenue is DRAMATICALLY increased and civs will want to trade with you, possibly applying a great diplomatic bonus)
Instead of the UP deciding on their problems at random or letting some more influential civ choose for them there should instead be a sort of raffle that lets the winning civ choose from certain categories (so it helps to have influence but it won't guarantee you anything)
I would say more... but I'd rather end it here for now ... and sorry if I repeat any ideas or if its already in place