What problems are you referring to that need to be "fixed"?
Starbases defenses, economy, and a few others I can't think of right now.
Right now, the big one that bugs me is the how ethics are set up. Its bad enough that *I will* research "Xeno Ethics" early in the game to minimize my encounters with them.
The problem is that good is needlessly punished for being good. The impression I get is that good is stupid and incompetant, while evil isn't. Its like good thinks that to be good, one must make ethinical decisions in such a way that it eliminates the possibility that someone can come along and say "wait a sec, they did that to do this for themselves.".
Lets look at one of these random events:
An in-depth scan of the planet's oceans has uncovered a small cluster of underwater cities enclosed in airtight domes. The inhabitants appear peaceful, but their underwater location would make the domes ideal for advanced research. What are your orders?
Good Option: Allow the citizens of the dome cities to live as they have - we have no right to interfere with their way of life.
Neutral Option: Condense the underwater population, freeing up some of the domes for research uses. (+20% Research bonus)
Evil Option: Dump the underwater pukes into the sea, I need room for my chemistry set! (+60% Research bonus)
Morality Weight: 4
Alright, so here, good leaves the inhabitants alone. No attempts at communication are made. No attempts at negotiating for the knowledge of how to build those domes. You don't even know if they would be willing, or wanting to leave.
Maybe the surface of their world was ravaged by some cataclysm and they sought shelter under the sea, never expecting that they could walk on the surface ever again. The devastation might of been so overwhelming that it would of been considered absurd to think that it would ever recover, so they never bothered to monitor things. Considering the lack of hyperdrive before humans came along, the idea that they could leave their planet would too be absurd. But if someone were to interfer with their society, that someone would be able to provide a devastated society with some hope.
In any case, I'm not argueing that every case needs a happy ending. Some situations can be impossible tasks. I'm also not saying to give bonuses to good right away in all cases. I'm would be satisfied if it were made possible to earn some these bonuses. The underwater colonist might offer to give you their domes if you were to build them a colony ship (which would be a special project), or they might join your society and will seek to understand how their ancestors built those domes in the first place, possibly unlocking a new tech, "Under Water Domes". These domes could provide a research bonus to certain planet types (ones with lots of water), or to provide additional terraformable tiles to certain planets (with lots of water).
What I'm saying is, I don't want to dread getting an ethinical event. I want to see them as oppertunities which, after a little effort, provide rewards, and not as ways to cripple my civilization.