I agree with most of these, especially number 4. The UI is not all that bad, but I feel like the intel screen doesn't do what I want it to do very easily. Its workable, it just takes more clicks than I'd like.
For me the hardest thing is bar quests: I want to do them, but checking where they are before accepting is painful. The fastest method I've found is to note the name, back out to the intel, go to the planet list, restrict to stars, then sort by name and scroll, then click (twice? don't remember) to show on map. It can take upwards of a minute to find where they are. At this point I just hit accept and then eat the reputation penalty if its not somewhere I want to go, which isn't the best.