Uh, I can't even find the ship list...
I've been stuck zooming in on the map and hunting down any dots that look like my civ's color.
If nothing else, how about making objects in the galaxy map buttons twinkle or blink when they're clicked to "on?" Edit: Also, especially if not only, the icons should be much larger in huge or gigantic sized games... Might only be necessary when they "blink" or whatever, but currently, they're almost invisible... I have to wipe the specks of dust off my monitor screen and pull out a magnifying glass to find anything.

Ah here's a good idea for it -- when an object button is clicked to on, disable the "ownership" button (maybe just for a second?), and make a big, red circle blink around all objects of that type. Woohoo! Oh wait wait -- make the circle around the object blink the color of the owner's civilization. I don't know what color to make the un-owned things blink... Maybe white, since that seems to be the default color, even though it's used by at least two civs (plus mine when I use a custom

).
But that's a bit off-subject. I don't know from MOO2 either, but I have found some aspects of fleet control to be difficult. Leaving ships in fleets while they're being upgraded could be troublesome -- it would be quicker, and provide defense for the ships being upgraded -- but can the fleet still move?
I agree entirely on DethAdder's suggestion for the colony management screen. Personally I use the single-Planet View screen, but I have the same problem -- it's difficult to see where the planet is. Simply moving the main window (the one you see when you close the planet screen... you know) to center on that planet would save me the time of hunting for it on the galaxy map.
Edit: Aha, and something kind of related to the original topic -- a fleet button on the map, of course.