1 - Fix a few of the broken missions I've encountered thus far, Breaking the planet is one of such.
2 - Auto Holster Weapons when beaming down to a non-combat area.
3 - A Walk toggle command, instead of having to bind it to a key. Walking helps with roleplaying immensely.
1 - A First Officer, Being able to promote one of your officers to first officer would be a nice touch. First officers would have to come with you on away missions and would have a unique set of skills.
2 - Fix the Crystalline Entity, I'm not sure how. Which is why it's in mid term. I have a feeling it will not be a easy fix either. But as it stands, the thing dies in less than 15 seconds. Heck, maybe for the first minute give it a 300% damage feedback pulse so that it stings anything that touches it.
3 - More Ship Designs, I hear this is coming down the tube. Which is fantastic.
1 - Time Travel. I'd love to see a mission where you travel back in time to interact with your former self and your former ship. This would likely be part of a much larger arc and likely be a nice long 4-6 hour mission chain in my ideal world.