Lots of the things I wished were possible turned out to actually be possible but it just hadn't immediately been obvious what the interface was.
I got a bit frustrated with sending science ships to research research projects before I realised that if you selected the science ship, you could right-click the orange box to order the ship to do the research (or shift-right-click to queue the research to do as soon as the ship completes its current order).
Probably at least one of the following are also already possible and I just don't know how.
I wish, if you'd previously visited a system, information like "number of potentially habitable planets and climate" or "number of celestial bodies" or "roughly what was on a settled planet" were available as "what you last saw" even if not in real time.
I wish the map showed you not just total resources, but showed the largest clump so you can prioritise building mining stations that gain 3 or more resources.
There's an alert that says when pirates settle in a system, can I please have a list of where that's happened? Usually it's obvious because I have eyes on a giant fleet coming towards me, but sometimes I want to make sure I know where all the original nests were and that I've got them all.
In fact, just a list of all the pop-ups and alerts I've dismissed would be good.
I wish it was easier to edit the action queue for a ship. (I was pleased to discover if you give a ship a new order, it cancels the pending actions but not the current action. IIRC "stop" cancels everything, and "shift-click" adds a new action at the end of a queue.)
It'd also be nice to be able to tell a ship "go here, wait till I have enough minerals, then build", but I understand why that's not as easy.
I wish it was easier to build a ship and designate it for a particular fleet. You can use the fleet "reinforce" option, but then I don't think you don't get to specify which ship is built or where.
These are all annoying but fairly small, since they're still developing, I think it's likely they will fix these eventually. I just felt better for writing it out :)
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