Brainstorming (read, half-thought out)
Ship design:
1). Fliping a hardpoint flips up-down in addition to fore-aft. (already mentioned).
2). Panning is good. But I often have trouble putting an extra on, because I can't get a solid view of the ship. Some free floating camera controls would be nice. I have a feeling there was some discussion of this during the beta, but I can't remember.
3). I'd like to upgrade the existing core designs. I understand, however, that they may have certain incosistencies for the sake of appearances (such as two colony pods but just 500 capacity), that make this difficult.
They might not be technically possible either, kind of a cheat ship to compensate for the lack of certain starting techs. I remember that from the beta, at least.
Perhaps with the advent of say, impulse engines, and better support, the game automatically introduces a Mark Two variety? Perhaps, a hidden, or fake mode for parts so I can design a colony ship equivalent to the base one that looks the same, with a nonfunctional pod since the base Terran design has two but only a capacity of one.

Diplomacy:
1). Tech trades: I'd like to offer an AI or human a technology for about half the normal value with condition they don't trade it to anyone else for say 50 weeks. Perhaps artifically inflating the value of the tech so they don't trade it, like a military tech. Or 80% value for a five week moratorium.
2). Money over time? Either I'm overlooking the obvious or this was removed for some reason.

Colonizing:
1). Ability to launch a ship from orbit with zero citizens aboard. I can't seem to decommision that colony ship from orbit, and even decommisioning a 1 troop ship is inconvenient. Plus, its out of character for a good civilization to jettison 1000 citizens into the depths of space.
2). A variation on the Rally command. Will bring up a list of unowned planets, and set a course in.
ALTERNATELY, just make it (obvious how to / possible to) use the ship/planet listing and focus without selecting or selecting without focusing. Maybe a couple of focus on only or select only buttons?
3). The core colony ship design for the terrans is fairly useless. With the standard starting techs and abilities, I can already stow an extra engine aboard for little expense and no sacrifice of range. Add an extra unit of speed, please.
EDIT: ADD #3

Slightly different ship naming process would make my life MUCH easier. As someone who upgrades ships regularly, I have to constantly rename them. Since I have not figured out a way to edit a shipname without erasing the whole thing (if there is even a way), renaming each one after each upgrade is a pita. Plus, I really hate adding some obsolete ship to a new ultra modern stack, which encourages me to rename them, which is a pita, etc.

Currently, default ship naming convention in the design screen is:

[shipname]
[Description]

and displays in the game as:

[shipname] [shipnumber]

A way that would make life much easier, but may exceed the 1 hour limit:

[shipclassname]
[versionnumber]
[description]

and would display in game as:

[shipclass] [versionnumber] [shipnumber]

When a ship is upgraded, if the default name is in use when upgrade occurs, the [shipclass] and [versionnumber] will be updated, but [shipnumber] could remain the same. If a player assigned name was given, no name change would occur.

Or, if [shipnumber] was a separate field, a player could assign it a name, and have only the [shipclass] or [versionnum] change. Sorta like the various Enterprise versions, and would display as BeamDestroyer C (or D, or E) Enterprise or some such.

Also, why not combine some suggestions here and add two small checkboxes to each ship's listed name in the ship design menu: One check box for Obsolete, one check box for delete. Check all the ones you want obsoleted or deleted, then hit the obsolete or delete buttons, and do them all in one fell swoop.

Plus, after a obsolete command the shiplist should not default back to "all", but stay in the "user" tab. Thats a teeny bit annoying.

Long Term Tweak:

Ability to upgrade ships using a shipyard rather than credits.

I would like an option in diplomacy to tell the AI to get their ships out of my space. Its annoying to see their scouts or something else just parked near my worlds. If I did that to them, they would be annoyed.

Someone above mentioned difficulty in removing items from ships in the shipyard. I've experienced this as well, but only when I try to use the boxes below the 3-D representation of the ship to remove them. I'll click on a part, remove it, then click on another part and the one I just removed is back. Removing components by clicking on them in the 3-D view works fine though.

What I'd really like to see on that screen is a checkbox option to hide jewellery parts in the row of boxes, so I can just add/remove functional bits when upgrading without having to pick them out of a long list of extras.

Colony Management Screen: Ability to purchase the planetary improvement. This has come into play for me alot since whenever I hit a monetary windfall I go through and purchase the first factory on planets.

The ship design feature is one of the most enjoyable features of Galciv2! The openess of the design is terrific! One minor improvement I'd like to see is the "lights" option. Make them translucent and blinking similar to the ships on Satr Trek Bridge Commander. Currently they are more like painted on spots.

I don't know if this is possible, but the Combat Viiewer is so enjoyable watching your custom ships battle, it would be nice to have the option to save the films like the VCR replays from flight simulators.

So, I've thought it over. Here's one that should be quick and easy, that I'd love to see.
The ability to color the fog of war/unexplored areas. Right now, I have trouble telling the difference between the black of space, the dark grey of unexplored, and the light grey of explored. I'd love to have the fog of war in say a dark blue or be able to customize that when I create my civilization/race.
Still though, just putting a toggle in the options for a red fog of war would work.

I dunno if this will get the green light now but you can keep it in mind for later if you like it... but I've been thinking about asking for resources to have their own color, habitable planets to be a brighter white than non-habitable. It doesn't show up unless you uncovered the "fog of war" so it doesn't eliminate need for scouting.

I was also thinking you could link it to some techs past Stellar Cartography.. like "Stellar Navigation" "Adv Stellar Navigation" "Superior Course Charting"

Maybe the last one gives a +10 to speed (which in game results ships get a +1 move ) .

Well, not bad eh ?

May have already been mentioned:
Upgrading:
1). Add a hotkey.
2). You know that "i" information window? Make it possible to upgrade there, so I don't have to seperate my stacks to upgrade.

Renaming (built ships):
1). Stupid blank field! Why allow the arrow keys to reposition the insertion cursor if the very first key I press is going to clear the whole name field? Possible tweaks: 1). Don't clear the name field. Make the player hold down delete. 2). Only clear the entire field if the user presses something such as Control-Backspace. 3). Place a 'clear field' button.
2). Allow renaming to happen via the 'i' information window.

It's hard to believe that not many people mentioned this before. But I tend to design a new custom race including ships every game. I find it very annoying having to obsolete all the previous designed ships from other custom races. I played one game as normal Drengins and they didn't seem to have the ships I designed as a custom race. So it just seems the game handles the custom races as one race when saving your custom designed ships. It's just silly having to obsolete all sorts of funky looking ships that were designed with another type of hullstyle enabled...

Perhaps all hulls of a certain size could be given the same number of anchor points so that items placed on other items would still connect properly.

More UP meetings, or maybe more than one thing to vote on at these meetings. I find it hard to believe that all the leaders of the galaxy assemble only once every 30 weeks (i think thats right) to discuss just one thing.

Also, the ability to select topics to come up for vote would be cool. maybe if you were president of the UP