Just some things I would like to see in beta 5, or before release.
1) Better space combat mechanics. The new roles of ships like escort, support, etc is pretty cool and I hope it works well. Also the different weapon ranges and rates of fire is cool, and I hope a good balance is found with that. One thing that really bugs me however is the current mechanics of weapon damage vs defenses. Weapons always hit for max damage, and defenses are really nothing more than some extra hit points for your ship vs one weapon type. This makes space battles feel very boring to me, like you know what the outcome will be 95% of the time before even starting the fight. I very much preferred how it worked in GalCiv 2; where weapons could hit for a variable amount of damage, and defenses could block a variable amount of that incoming damage. It made it feel exciting to watch a battle and see those "lucky" shots that hit for max damage, or breath that sigh of relief as that gauss round that would surely be your death just happened to hit a strong-point of your armor and bounce off harmlessly. The space combat in it's current state for GalCiv 3 does not provide any of those moments of excitement. It is prettier than GalCiv 2, but boring.
2) Logistics points of ships. When I have a ship selected I would like to see how many logistics points it uses in that info box at the bottom left of screen please.
3) Fleet movement points. When I have a fleet selected I would like to see how many movement points it has in that info box also please.
4) I would still like to be able to select the placement for my colony capitols.
5) A better more challenging economy system. Set the circle slider to max production/research. When low on cash research straight to Tourism and "win" the cash flow game. I haven't even bothered to establish a single trade route with hundreds of hours played across many different games 
6) The shipyard lists. Please please please PLEASE get rid of the hundreds of reappearing M0 ships every time we research a new tech.
7) Ideology. I still really don't like that I can max out the benefits for Malevolent and Benevolent. I could see maybe maxxed Pragmatic and Malevolent, or maxxed Pragmatic and Benevolent. However common sense just tells me any society where the government is attempting to impose such radically different ideologies upon the citizenry, is going to end up in a state of civil war at the very least, and probably sooner rather than later. Or the people would just rise up and "remove" (in one way or another) the obviously insane madman running the nation/empire/government.
8) Tooltips. I would like more accurate info in the tooltips and better descriptions. Especially with things like buildings that are one per world, or one per civilization. Also it would be nice if the clipping got fixed. It doesn't do much good to have a tooltip with helpful information about what something does, when you can't read half of that information 
These are some of the more common things I have run into for my GalCiv 3 wishlist. Number 1 on this list is close to being a "game breaker" for me. The space combat just feels too stale and predictable. I still enjoy the other aspects of the game enough that I will continue to play, and probably get all the expansions, for a long time to come. And yes I know we are still in beta, and all of these things may be getting changed/fixed as we move forward 