The sidebar queue that allows quick access to planets, ships and starbases adds new entries on the bottom of the list. Which is a bit counter intuitive since the last acquired ones are usually the ones you frequently have to get back to.
For example when you're a few turns into the game and already have some ships to defend your planets. When you start building attack ships and transports you don't get any warning that they are done. Not that there is any need for that, but it would be nice if you could see they are ready by glancing at the sidebar instead of having to perpetually scroll back to the end.
Planets tab : The option to attribute a group or usage category. So you can quickly and easily add in orders to you bigger fabrication oriented planets.
Ships tab : The option to upgrade ships from there. Be it individually, by planet, by stellar system, or every ship of that type. With an option to also include older models from the same type.
An option to light up the minimap to show the level the starports are filled up (and with what type of ship). In order to spot possible weaker spots. Something that you could also see for other factions through some spying.