I've thought about the game a bit and found the following the enhancements might make the game even better (at least, to me):
1) Space combat:
As it is now, most players (and all the AI I've encountered) just puts weapons on ships and ignores defenses. With good reason once you look at the math behind the system. The higher the attack value compared to the HP of the hull, the less useful defenses are because the one shot-one kill event is more and more likely to occur.
Suggested change: change the way defenses work.
Instead of using a matching system, let defenses work autonomously from the type of attack. Instead, they should boost the ship. This could be used so that certain types of defenses favour certain types of hulls.
Example:
- Shields: work as defenses used to. They recharge after each salvo/round/whatever you want. They work to full effect no matter the type of attack (beam, mass, missile).
- ECM: works as a dodge. Each time a weapon is fired, it tests to see whether it hits or not. If it hits, the other defenses are applied to calculate damage, otherwise, damage is ignored. This will help keep defenses useful for little hulls where the old-school defenses would have little use. This type of defense should favour smaller hulls.
- Armour: boosts HP. Plain and simple. By boosting HP, old-school defenses (such as those proposed shields) become more useful as the attack/HP ratio improves.
2) Starbases:
Fleshing out starbases is a time-consuming hobby. One way to make management easier is to make constructors works as miners. When new modules are researched, constructors fan out and improve the starbases themselves. No longer do you need to be build fifty-odd ships to complete a starbase. In exchange for this, improving should take time and possible also money.
3) Influence starbases:
Influence starbases act as embassies and forums (fora?). The way they work now, you build a couple (or dozen) of those in your neighbour's influence sphere and try to flip planets. Obviously, this is pretty much a passive declaration of war and lack of a sufficient military machine will see your latest washed jeans model answered with a plasma bolt.
I think they might become more interesting if they not only boosted your influence in its range but also allowed that influence to spread out. When a colony grows and matures, its sphere of influence expands, centered on the planet itself much like a well or a source. What if influence bases could boost those wells so that colonies have a greater reach? Or what if those bases could act as 'wells' themselves, with their power being the influence present boosted by their modules?
4) Influence
Mostly, influence is a source of tourism and a reason to be disliked. In fact, unless you have an impressive military, it may do you in. In my humble (and not very expert) opinion, influence could use a bonus or so. Perhaps planets in someone else's influence sphere would take a morale hit, or the nation as a whole might take a morale hit when facing the loss of their only source of I-Pods.
5) Politics
Now, people just drop taxes the week before the elections to get re-elected. Then taxes are raised again until the next elections. While this is pretty close to what happens in real life

perhaps we could make the level of taxes a more engaging choice.
By making the election result a mean of morale during the last year, these kinds of exploits would be removed.
Also, I'd like to see the rewards be more flexible depending on the degree of freedom in you political system. The bonus you get shouldn't be determined at the beginning of the game such as Federalist: +20% economy. Instead I'd rather see the bonus depend on the election results so, Federalist: economy 1% * every ten percent over 50. That bonus could be improved by having a more advanced political system.
6) Allies
Not only should allies strife to enter the same wars, they should also strife to make the same peace treaties. Whenever an alliance is in war and one of them wants out, they should offer a peace treaty that includes peace with the other members of the alliance.
I've been dragged into wars I could handle as part of the alliance but when my partner made peace, I was suddenly facing an overpowering enemy who suddenly didn't want peace anymore because the odds got a lot better. It'd be nice if the ally would consult its friends first see who wants to keep fighting and who doesn't and then negotiate a peace treaty for all those who want out.
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Well, that's all I could think of for the moment. It's likely many suggestions won't be very much liked but I just wanted them spilled out. If you read this right to the very end, I salute you.