I've played three or four (single-player) games now and there are some things that really bug me about the way the designers have set things up.  I just thought I'd toss two of them out here in the hopes it can stimulate some ideas for improvements in later versions or expansion sets.

1. AI's and missions.  The idea of having the chance to work with another team is great, but the implementation is so random and inflexible as to be almost worthless in my opinion. There are several problems here. 

a. First, the missions system should be tied to the relationships you already have with other players and to events actually happening in the game.  For example, the entire concept makes no sense with a race against whom you are actively at war.  I'm sitting there pummeling a player, methodically taking over one planet after another, and with one planet left, he pipes in, "There's work to be done. Are you interested?"  Hey look moron, I'm busy committing genocide against your civilization so I'm probably more interested in that right now.  Then I looked at what he wanted me to do and it was to destroy infrastructure of another player with whom I had an alliance. I'm sorry, but that's just absurd. If the missions are totally random, with no relevance to the actual game, then it doesn't enhance the game... it's just background noise.

b. The missions seem to be the only thing that matters in your relationships with other races.  That's completely unworkable because, first, the missions are so random that you often can't do them no matter what and second, there are other things that allies do for each other and those should get credit too.  For example, I am allied with another team with a planet near my territory.  He has a small force there that gets attacked by an overwhelming force from a third team (four teams total in the game).  He calls for help and I send the bulk of my fleet to save his planet.  That's what allies do for each other after all.  Now it's costing me ships and time to fight this lengthy battle, but I do save his planet.  In the meantime, in typically random fashion, this same ally has given me a mission during this battle to go destroy structures of the team that's attacking his planet.  Of course, I can't do that because I'm busy saving his sorry a$#.  So about a minute after I've saved his planet, he says he's disappointed in me, says the alliance isn't working out, and breaks off relations.  That just makes no sense at all.  If the designers can make the AI's smart enough to fight complex battles, why can't they make the diplomatic system smart enough to take game events into account when evaluating alliances?

c. The entire missions concept, as implemented, presumes the human player is the galactic whipping boy.  I'm supposed to run around and do things for everyone else, and I can't trade with them or be at peace with them if I don't.  Huh?  If I'm supposed to spend all of my time doing things for everyone else, I obviously have no time to build my own empire, so why can't they ever do anything for me?  Why can't I assign missions to the other players?  For that matter, why can't I decide for myself whether or not to even entertain missions from each other player (or at all)? 

d. The bottom line for missions is that I just ignore them and I consider myself to never be in an alliance any more.  My favor with other races comes and goes because I happen coincidentally to do something that someone had asked me to do, but I just ignore them and consider everyone my enemy.  It's really the only way to survive since resources you spend trying to placate an ally will just be wasted later when you're unable to run off across the system to do some lame random task for them.  For that matter, when I did try to have alliances, never once did an ally ever help me out.  I thought once that it was going to happen, when I was being pummelled by an enemy.  The game said "allied forces have arrived to help" or something like that.  Yeah, well I guess if you consider one scout ship flitting through the system to be help, then that was nice.  I can see how the alliance system would be great for multi-player games, but for single-player games, it's really worthless.

2. Percentage basis for number of ship points.  Okay, I get the idea of taking more and more of our income for maintenance of more and more ships.  That makes perfect sense.  But what doesn't make sense is that no account is taken of the size of your empire when deciding how much to charge for your ships. You pay x% of your income for y ships regardless of how large or small your income is.  Maintenance of 20 ships of a given type will cost more if you own 10 planets than if you own one because it is charged as a percentage of your income.  This doesn't make sense.  Early in the game this isn't much of an issue, but it's a significant issue later.  As you own more planets, you need more ships just to sit at each planet and protect it from small maruading forces.  More planets... more ships.  But the only way to get more ship points is to give the system a higher percentage of your income. Paying for ships should be on an actual credit/sec amount.  If you haven't enough credits/sec to maintain more ships, then you should have to make do.  If you have more planets, and more income, then you should be able to have more ships.

Okay, that's it.  There are other things that I would tweak, but these are the two things that really spoil the game play for me.  I don't know if my view is one shared by many others or not, but there it is.