Well, my biggest issue is still the various (and numerous) problems with the game after loading a save game which are detailed in several other posts. I would think this should be a very high priority, but then again, I'm not crashing to desktop

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I think this game has the potential to be the gold standard for space strategy, but I have to say I'm disappointed with the number of bugs that I'm seeing. On to the bugs...
1) If you remove items from the end of the scroll list in the ship design screen, it doesn't update the list and the deleted item is still visible, but obviously can't be deleted again. It makes from some really odd behavior until you figure out what is happening. The items at the end of my list were modified hardpoints, I didn't test with normal components.
1a) While on the topic... this is a request. If you modify a hardpoint on a piece of a ship, and then try to remove that piece, it won't let you until you remove the hardpoint modification. I'd like to suggest that if a player tries to remove a piece and the only thing preventing him from doing so are modified hardpoints on the piece, just remove everything instead of telling me you can't remove the piece because things are attached to it and forcing me to individually remove the hardpoints. Wow, that was a long sentence...
2) I have a save game with the following bug. You load the game, go to the ship design, select a particular ship and upgrade it. You can remove pieces, but as soon as you try to remove a modified hard point, matter of fact, as soon as you click on the modified hardpoint in the list, the entire ship resets back to its original state. This makes it impossible to actually upgrade the ship, at least in the way I wanted. I ended up having to make a new ship and pretend it was an upgrade
3) When ships are stacked, there are several instances of incorrect behavior as you attempt to move them. Sometimes multiple ships in different areas remain selected after the move. Sometimes the information displayed is not for the ship selected. Just stack some ships and then try to move then individually.
I won't get into the various deficiencies with the fleet interface and not being able to do things to individual ships without disbanding and moving them first. That's been posted several times already.
4) I'm positive that the checkbox for 'Don't throw away unused move points at the end of an auto-move' isn't working. But then, as I thought about it, I'm not even sure how it could work. Since automove occurs at the end of the turn, even if there were points left over, the ship would be restored to full movement points with the beginning of the next turn before you had a chance to move it. So, maybe it is working, but what's the point?
There were lots of other bugs, big and small, that I've seen, but these were the ones that come to mind this morning.
Thanks