Just a dump of notes I jotted down while playing earlier, not in any particular order.
Every dialog exchange ends with a "goodbye" option, then is followed by an additional "Close Communication" prompt. I'm done, don't make me click twice to close.
Further on that, the lack of a shortcut to exit an exchange is annoying. Don't make me back through multiple levels of the dialog tree to exit, when I'm done I'm done, let me cut it short.
Further further, save points and nested quest updates in dialog do not play nicely together. Some exchanges end with combat, if I die, my only save point is before the dialog, and I mindlessly click through the options again to get the updates. Die again, repeat. I'm not sure what the fix is here, but this is monitor punching material. I suppose an auto-save at the start of combat would work, but you're still stick with forced repeats of dialog if you need to load an earlier save and come back later.
Hitting escape or tab cancels the autopilot, it shouldn't.
Hitting escape to leave a planet with the lander is annoying. Let me access the menu.
Fleet combat screen one click front and center surrender button is a bit ridiculous. I mean, my fault I guess, but sometimes I see that screen and my brain skips directly to clicking it, game over, back to the last save. Happens more often when I only have my main ship, the screen less like a selection and more like a "click to start battle".
I think it depends on other conditions and is likely a bug, but I keep having ships randomly fly up to me to initiate an exchange, with the only option being "hail". Thing is, they don't want anything, they're not attacking it's just some random NPC I've had quest dialog with previously, but there's nothing new. Just time to leave the conversation and continue what I was doing. It's especially annoying when it interrupts autopilot.
That pathfinding for autopilot takes you in the exact direction of your destination, as opposed to the nearest exit into hyperspace, is rather annoying. Bonus points if starbase hypergates could be pathed through automatically.
The system used to show the labels on a planet is frustrating. What is it, the closest orbital line? Give me a hotkey to show all the names at once, or even a mouseover tooltip. Don't make fly all over the place to check which one has the name I'm looking for.
Being able to click names of things from the log to trigger the autopilot is great, except I don't know where it is at that point. When I check the map, I can't see the name anymore, and the autopilot is cancelled. I have to write them down, search for it, and set the autopilot again, making the links a bit useless. Rather than prompting for autopilot, the links should open the location on the map.
In general, a lot of the "in-system" routine trips are annoying. Like flying back to earth to re-crew, or visiting my allies homeworlds, it's all dead time. Let "known contacts" be accessible from anywhere in the system, disable it if anyone is hostile. In system flight is slow, please don't make me wait on it for nothing.