I just wanted to add my voice in, there are a few things I mentioned in past posts and would like to expand on them here.
You may already be planning some or all of these changes...if so, disregard.
1) System indications with respect to missions in log
I would suggest that the icon in the system list, or the name of the system should be a different color, like perhaps Blue or Red.
On a side note, I would also suggest that the actual title box for missions be colored by difficulty in your "current" and "available" windows based on your level.
2) Circle over galaxy map sector for primary mission selected
I am requesting that you add a circle, much like you use in the ground or station/ship missions that shows which sector your current primary mission is located in. This will make finding the sector needed MUCH easier.
3) Remove sector space travel for connected missions
It is silly to have to exist to sector space, physically find and set course to the next location with directly connected quest lines.
Note, I do not mean multiple system quests...the connected quest lines, like one where you chase a ship to another system, or pursue star charts, etc. You should transition to the next system right from the system you are in.
4) Random encounters
Random encounters should not be the huge fleets we see all the time IMO. Not only is this a bit silly (200 to 300 Klingon ships flying around in Federation space might raise more of an alarm) it is just not very Star Trek. It is more likely that a large fleet like in the current random encounter would be in a static place in the area and remain so, and the random ship encounters would be one ship, perhaps 2 at most.
And that ship would not always result in combat. Sometimes you could outthink your opponent...much like the breen mission where you rescue the "recruits" from the breen ship by masking the sensors.
Thats it for now. You guys did a great job on removing astrometrics, space travel looks fantastic with it off.