I have a few complaints about some of the exploration missions that I have done along with some thoughts on fixes.
Problem 1) I get a mission to check out a planet that projected a beam into space and hit a ship. Upon beaming down to this planet, my away team discovers that the beam came from a planet defense system and we should disable it. Looking around, there are a bunch of buildings that don't look like they are abandoned. So I am suppose to disable this planetary defense system of this alien race leaving them open for attacks just so we can pass through the system without worries?
Fix: If these planets are no longer inhabited then how about making the buildings look like ruins or just like crap?

Problem 2) The Borg missions. I have run into a few where they say 'I' instead of 'We'. Right now I am on one that says that the Borg wiped the computers but some personal logs remain. Borg have personal logs? When did they start keeping diaries and journals? Also the Borg base that I am suppose to be in does not look Borg at all. Another thing is why would the Borg build a base underground on an inhabited planet with a pre-space cult rue?
Fix: I am not sure if these are just randomly created dialog and picking species or what. Make sure the dialog matches the species and maybe making these random bases look like they belong to that species as well. So if the mission picks Borg for the species it also selects a borg texture set for the base.

Other than this and a few other things, I am loving the direction that the game is going. Keep up the great work.