I don't know if this has been mentioned before but here a few of my ideas:
1. Make population be more important to the ability to construct ships/units for example World A has a population of 400 million while world B has a population of 8 billion, YOU want to raise 400 troop units and a Base ship but in SEIV you'd only go by which world would build what faster...
Instead I was thinking maybe have troops and ships cost population as WELL as the money so say a base ship costs you 1 mil population while 100 troops costs you 1 mil
SO when world A builds the base ship it will have a population of 399 mil left
And when world B finishes the 400 troops it will have 7.6 billion people left because you hust raised 4 million people into your armies.
I don't know if I worded that correctly but I would just love to see a planet's population that actually matters to what you can do with it.
2. I would like to see TRACTOR BEAMS muahaha, no seriously I would like to see Non-combat tractor beam projectors so that you can rescue crippled ships or tow a crippled enemy ship back to your base so you can board and capture it. I mean I'm sure we've all seen that jewel of enemy alien technology that was crippled by another player and go "I WANT IT SOOO BAD!" but lose it because we can't two it to a base.
3. Better planetary militia: I mean I know they are not supposed to be able to stand up to troops but I really enjoy those planetary invasions where it becomes a real nail biter and I'm going "Can my troops pull it off" right up until the end.
I would also like to see planetary milita count as a certain percentage of the population.
4.Pirates!!! I mean random alien "or your own species" pirate ships come out of nowhere and raid a world or two and not have them tied to anyone, And say every now and then a pirate fleet comes out of the warp and invades a planet or two so that you can actually have to send out your military every now and then to retake your own worlds or just to counter the occasional pirate threat.
5. FTL drives: I'm talking short range warp point openers that you can place aboard your ships, say make this tech come along in the late game and only have a range of like 50 light years or something.
It's just that I'd like to see this because once you get warp point openers they can open anywhere in space unless you have those gravitic shields but that also ruins YOUR ability to warp so I think just making a short range ftl drive would be better for everyone.
6. Deathworlds! Okay maybe this sounds dumb to you guys but I'd like it if say every now and then you find a world where everything wants to kill your colonists from the animals to the plants and that this way
you'll have to use some security force or something to help with the initial colonization and [b] okay if your colonists survive after a few years the population gets bonuses say in maybe reproduction and strength and the like....but anyway this is just a sort of random thing.
7. MEGA sphereworlds: Okay say you have a trinary system and you have all 3 stars with sphereworlds around them I'd love LOVE to be able to connect all three of those sphereworlds and make a mega structure that dwarves other sphereworlds and becomes something that would take dozens of troop ships to capture and all that fun stuff 
8. Real TIME battles would just be a lot more fun in my oppinion depending on how they are run I mean i hate it when I have 3 troop ships loaded with soldiers but I can't capture a world because it kills off each troop one at a time and regenerates it's milita for the next force of troops coming in.
I want the ability to drop all 3 troop ships on a planet if I so choose.