Thanks for the feedback, pmuscles! It's always nice to see GalCiv1 players chiming in on how the sequel is coming. 
Oh, and be sure to update to 4d...I beleive it resolves some of these issues - and most likely introduces some new ones 
** Major Bugs **
1.) Noted.
2.) Yeah, right clicking will work, though if we have time we'll work up a system that auto-deletes them as necessary.
3.) constructors: You shouldnt be able to construct a starbase in a tile with other ships on it. This is by design.
Individual Ship Stats: We ccan make this info more accessable.
4.) YES! I want this too...but have been swamped with major features to get in.
We should have it working soon (Though it won't work when a game is in progress, since at that point it's functioning as a save/load screen.)
5.) Alphabetically should be easy, but getting in tabs will be more work.
As for alien ships showing up in your list, this will get fixed ASAP (and may already be fixed in 4d).
6.) The entire upgrade system is in for 4d...and please be brutal on it. We need to weed out as much cheese as possible before gold.
7.) We're still batting social governors around. We'll see what makes it into the game 
8.) Interesting...this one slipped under my radar. We'll get these saving.
** Minor Bugs **
1.) Should be fixed in 4d.