Here are a few of my suggestions to improve this game...
1.) If I press the button to "beam me up" or "warp to sector space", just do it, I don't need to be asked "are you sure?".
2.) If I double click on a star system, move there. Again, I don't need to be asked, "are you sure?"
3.) If I've double clicked on a target (star system or region) and I come close to some other object, don't stop and ask me if I want to enter. Bring up an option to interact with the new object while I'm with in range.
4.) When I talk to a quest giver, don't stop the movement of my ship to another star system.
5.) Place a "close window" button on the quest window.
6.) Be consistent with the scan button (and other similar action buttons) . Either place the button in the middle of the screen or on the lower right hand side of the screen, not mix and match.
7.) When "beaming down" to a friendly zone (Sol Star base, Memory Alpha, etc.), automatically holster the weapons.
8.) Even though it's more realistic to make "filler" NPCs solid and to have us "bump into them", please make these "filler" NPCs pass thru or don't penalize our movement so much when passing them. FYI, "filler NPCs" are those NPCs you have wondering around Sol star base, etc and there is no interaction with them.
9.) MMO's have been around for years, we shouldn't have to suffer spam from "gold" sellers. At least help us easily get rid of spammers. Example, put a "Report as spammer" button in our mail window and make it easier to report and ignore spammers in the zone chat window.
I think this will do it for now. I hope this helps. I know if you implement my suggestion it will make the game more enjoyable, for me and possibly others.