Ok, hopefully somebody will see this. First off, I finally got around to buying the game, and, boy, what a massive improvement! So "Well done" to the developers and play testers! I am loving this game more and more... might top Master Of Orion

...it already does in may ways, but MOO-II is still a faster-paced game (less time to play) and has better user-interface - not by much though - thanks to all the improvements in Galactic Civilizations II.
Again, I am very pleased with this new version!
A patch just came out (1.3A), and I just installed it. I have not yet seen if this bug was fixed by that patch.
What is happenning is the planet icon is appearing in the orbit box (becomes "Stacked Ships" box when it is not supposed to be) with newly built ships (transport ships, mostly, not those enroute either - but I've had other ships get "stuck" too). This makes the ships impossible to select. The work-around is to destroy the ships. They then sometimes appear in the normal ordit window without the planet being there messing things up; the planet isn't a ship (lol). Setting a gathering-point doesn't always solved the problem either - and the planet can't be selected in order to tell it what gathering-point to use if the bug is active. This bug happens at planets with freighter routes connected to them (I think so, anyway). I hope I'm explaining this properly and I'm guessing others are seeing this bug too? Trying to select the planet and ships into a fleet will crash to the desktop.
Edit... I loaded the game and tried to see if the bug would happen... an existing bug of a planet and ships stacked, well, it is still there, but maybe it won't happen in a new game? If not, then this bug is not yet fixed.
Here is a little of the debug report:
Debug Message: Loading FOW Map
Debug Message: Loading ZOC Map
Debug Message: Loading Planets
Debug Message: Loading Stars
Debug Message: Loading Anomalies
Debug Message: Loading Resources
Debug Message: Loading Civs
Debug Message: Loading Colonies
Debug Message: Loading RallyPoints
Debug Message: Loading Ships
Debug Message: Loading Fleets
Debug Message: Can't find ship type Fleet in definitions
(it repeats this line over and over)
So, yes, a planet is not a ship.... so crash it goes...
Also, another bug? The mini map sometime messes up where the present location viewer window becomes as a paint-bush, and then paints the mini-map window blue as the player moves it around. Solution. Save and restart.
Those are the only bugs I've seen so far.
A few other comments:
Only one serious suggestion, really, have the gathering-points assignable from the civilization (planet) manager screen (after giving the destination in a pop-up, have the program return BACK to the civilization screen so the player can contiue from that point.
Also, it'd be nice if the gathering-points could be managed directly by accessing them (via a manager pop-up) from the main star map - via selecting an icon. Provide a way to delete gathering points instead of making the user go to each manually on the star map. If there is a way to do this, I have not noticed it yet.
It'd be nice if selecting the planet name (or something else specific like that) on the planet manager screen (civ manager) took the player to the planet's location on the star map (exit the manager), not into the planet tile arrangement screen. Keep that feature also, but as a seperation icon on the planet manager screen for the associated planet.
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So, again: VERY WELL DONE to the developement team on this new edition! A lot of the changes are very enhancing to game play, and make sense! I'm very happy with what you all have done with this game as a your customer.