2) I actually hadn't thought of that but it does make sense. Though, aside from the extra work I'm sure it would take you, I don't see why not. Populations are supposed to fluctuate naturally after all.
3) Always good to hear ^_^
4) Ah, I'm still pretty noob in the game so I actually didn't know that XD What about the price over time for the ships though?
5) Haha well yeah in the hands of only one species I certainly see how that could be a problem. You may have a point about the standard galaxies but I don't see why people wanting to ally themselves with friends is a problem. Even so, it would still be a risk on their part to explore too far out leaving their planets and scouts exposed. Expansion always has to be balanced with the ability to defend the newly expanded borders. The last point is a good one. I'm not sure we want to do that. I'm a pretty active player but I understand not wanting to base balance around how often one can log in.
Maybe you could add some sort of 'exploration cost' to claiming planets beyond your established border. Might slow people down enough to allow the slightly less active to keep up. Especially so early in the game when resources are tight as it is.
6) I'm sure this one would probably cost you a good few hours of work lol. I mean I'm not a programmer so I don't really know how all this stuff works but I understand that implementing something entirely new like that could be taxing. Especially since I've got the impression that your're already pretty busy.
7) Yeah, lots of possibilities there.
Oh, trust me I am full of ideas. I've always enjoyed thinking up new concepts for games as much as I enjoyed playing them.
Couple new ones off the top of my head.
8.) Map trading. Something like in the Civilization games. Might be able to do this instead of #5 even or something to add even on top of that but all for the same purpose. The galaxies always feel so small to me and I want to know what's out there. I don't know about other players but I like knowing what's around me. Maybe it's intentional, because it does add a hint of mystery to each galaxy, but exploring the unknown could be just as fun.
9.) Open Passage Clause to NAPs. Again similar to that in the Civ games. Allowing friendly alliances passage through your territory could open up a new level of diplomacy.
10.) This one is a bit of a heavy idea. I think it would be neat but definitely seems like it could be a lot of work. Basically, being able to further micromanage building construction and battles on each planet. The way I see it is when you go to build on or attack a specific planet it opens up that planets surface grid. In this way, you choose where you build each type of building on the grid when building and when attacking it opens up an all new level of battle into the game. You could have a landing force consisting of a number of soldiers that you recruited out of the population and trained in the same way you pay to build a ship. When you deploy a landing force on the surface of the planet you start in a selected grid or even multiple locations depending on your strategy. You command where they move and conquer first. This would also open up another way to individualize each species since you could give each species a unique ground battle bonus. I have some ideas on that as well.
Drall: Biological Warfare: Drall infect their targets with microscopic biological diseases that cause additional casualties and deaths after each battle. Infected casualties can continue to spread the diseases forcing the enemies to separate their casualties from any heavily populated areas.
Unique Unit: Creep Colony: Creep Colonies don't directly contribute to battle. Instead they stay behind the lines and focus on reproducing, providing their forntlines with a steady supply of reinforcements.
Gorgoth: Gorgoth Ferocity: Gorgoths battle score is increased when attacking.
Unique Unit: Goliath: Goliaths are the elite born within their populations and raised as killing machines. They are all around better at battle.
Ji: Territorial Instincts: When defending their own territories, a portion of the local Ji populace aid in the defense of their homes.
Infectious Blood(No unique unit, instead a second passive bonus): A portion of fallen Ji infect their killers via their blood with a rabies like virus, causing additional casualties. (Does not spread like the Dralls Diseases do however)
Kreel: Predators: Kreel forces are slightly rejuvenated by feasting upon fallen enemies.
Unique Unit: Rogue: Kreels advanced stealth technologies extend to the battle field. Squadrons of Kreel rogues can sneak behind enemy lines and attack where their enemies are weak. However, once revealed their chance of escape is limited and even further hindered by the planets scanners.
Oomari: Psychological Warfare: Enemy forces have their battle score reduced by a percentage.
Unique Unit: Telepaths: Telepaths have extremely low battle scores but aid their allies by causing enemies to hallucinate, effectively reducing their chance to cause deaths.
Shy'Dow: Invasion Mastery: Shy'Dow battle score is not effected by the planets habitability rating.
Unique Unit: Titans: Heavly armored soldiers that have a significantly reduced chance of being killed. However, due to the amount of armor they carry, their ore cost is significantly higher.
Sirnef: Unified Mind: Due to their connection with each others minds, Sirnef can better focus their fire. This results in a higher death to casualty ratio than other species.
Unique Unit: Battle Bot: A Sirnef whos construction design is aimed towards battle. They are individually extremely powerful but do not receive bonuses from Battle Tactics or squadron size.
Toag: Mercenaries: Toag offer to spare the life of their enemies populace in exchange for their service. A percentage of the conquered populace will instead be converted into mercenaries.
Unique Unit: Mercenaries: Toag can pay to instantly hire mercenaries(Basically any toag willing to make a quick buck) instead of waiting to train professional soldiers. However, mercenaries are more expensive and less effective.
Turian: Last Stand: Turian battle scores are increased proportionally to the amount of remaining land under their control on the planets surface. Turian forces moral is not reduced if their enemies control more land. This bonus only applies when defending.
Unique Unit: Marine: Marines are highly trained soldiers taught to take advantage of their enemies weakness' allowing them to fight on even ground with even the fiercest of opponents. If marines are fighting against a stronger force, the enemies battle score bonuses are reduced to be equal to that of the marine squadron. This reduction in battle score applies only in the calculations in exchanges between enemies and Marines and does not apply to the rest of the Turian forces.
Zeeb: Base of Operations: Zeeb can construct bioformers, scanners, minefields and planetary shields on lands under their control and not currently in conflict on planets they are conquering. On their own planets, construction projects will not be effected by battle.
Unique Unit: Battle Technician: Trained in both the art of combat and construction. Battle Technicians are used to fight as well as build Bases of operations behind the lines. The more Battle Technicians, the more buildings they can construct per tick. (Up to a maximum of 10 to keep in line with normal construction rates)
The battles would take place in sectors. Each sector would consist of a number of grids(perhaps 10x10 or w/e Though not all would necessarily be the same. This would make some sectors on the planet more valuable making them prime targets for attack and defense). Each grid is equal to 1 land. Land units can move one sector per turn. Control of a sector gives control of all grids within that sector. Any construction projects in grids within sectors in conflict are halted.
Base battle score is 100 per unit. There would be a new technology(Battle Tactics) to increase this. Battle score is increased by an small but increasing percentage the larger the squadron is. Squadrons are simply the units within the same sector on a planet. Death to casualty ratio is determined by the difference between each sides Battle Score and Battle Tactics tech level. Battle Score can be increased and decreased based on moral and the current habitability rating for the each species. Moral is determined by consecutive victories or defeats, difference in army size and difference in the amount of land under each sides control.
Yeah, I could keep going, giving more specific details on everything but just for the purpose of getting the idea across I think I've more than accomplished that XD
Also, hope I don't contribute too much to frying your brain

Last thing I want to do is make your job more difficult lol.
Edit: More ideas:
11.) Alliance Standards: Customizable flags to represent your alliance
12.) This one is more of a bug I think. When you customize the colors of your planets and allies planets, they get mixed up between the new map and the star map on the main profile page(in one ally a might be light blue and ally b might be dark blue but in the other ally b is dark blue and ally b is light blue). Also, the color of star ships don't change. Made my systems green and my allies blue in the last galaxy then got confused because my ships were still blue and theirs were still green.
13.) Map Borders: Purely aesthetic but could be neat. A drawn border around each alliances controlled zones on the map