As well as most of the stuff already mentioned the one thing I want the most is the ability to RETREAT, it is silly that my ship with 6 move and 4 remaining cannot retreat from a 2 move baseship that happens to attack from the main system map. Moo2 allowed you to warp out, so did BOTF. It was the one thing that confused me about the game when i first played it, searched the manual, looked at all the buttons, and then my colony ship got fried by a frigate. UGH.
That and the no 'good' random events and lack of personalities (captains and ministers) for the planets and ships.
------------------
"The Empress took your name away," said Chance.
Owen smiled coldly. "It wasn't hers to take. I'm a Deathstalker until I die. And we never forget a slight or an enemy." -Owen Deathstalker.