Space: Autofire for all beam and cannons (fore and aft). No autofire allowed on torps / mines and "Chase Cam" for your ship, useful especially when using cannons.
Missions: Move as much dialogue into one page as possible, seriously it is silly having a quarter of a page and then having to click continue just to see a few more lines of text. Also, dont drag out dialogue for ground encounters by asking someone to scan one item, and then 3 more and THEN one more. Dialogue that asks for one and THEN 4 more is better than 1 + 3 + 1. Its just silly otherwise.
Exchange: Allow the search results to be sorted in ascending / descending order by column (price, name, etc).
Greater depth in ground encounters, requiring the use of tactics and involving mini-games e.g.
Engineer: remember pipe dream? Well imagine having to reconfigure a circuit system within a time frame.
Tactical: Imagine a ship infested with metallic spiders which are trying to destroy ships subsystems. Enough spiders have be destroyed within a specific time period in order for the engineering team to complete repairs.
Science: Imagine a computer display with broken DNA strands. The player has to link the correct configuration of DNA strands together to form a complete one.
Quest dialogue and tutorials: Make sure the sector and system names are detailed in each Missions text. Including where Romaine is.
Introduce a balanced death penalty system, and stop the patrols in the sector space encounters from camping spawn spots. If someone is in a spawn area, they cannot be targetted and cannot target an npc.