I would like to see interstellar travel
It takes light, traveling at 300 000 km/s, 4.6 years to reach the nearest star besides the sun.... your ship travels at a messily few km/s. It would take so long that your UMmu would (forgetting the usual logistical problems like food and life support) die of old age before you got there xD
Not to mention having to wait a whole year at maxed out time acceleration to actually get there.
A more interesting thing tough would be collision detection so modders can write support to damage or destroy your ship on impacts with other ships.
Another thing that comes to mind is a more filled up solar system. Granted, that can be created already... I'm thinking about more stuff then just the sun and planets... I'd like to see comets and the asteroid belt...
Separation of the physics engine and graphics engine would be cool... and plugins for the graphics engine would be good so that Martin can focus on the physics engine and let some of the graphics effects be developed by the community.
A mesh for the sun in addition to the sprite.
More accurate physics and more physical phenomenon.
More accurate planets and atmospheres... Come on! The gas giants don't really have a solid surface, do they?!
Also, I'm talking about real weather. Changes of air temperature, pressure, humidity,... different weather effects ranging from the slightest breeze to category 5 hurricanes

(Hey, if you can make the specular reflections, you damn sure as hell can increase the strength of the hurricane over warm waters).
Real clouds... not just a thin layer at what? 7 km altitude?

Clouds that would affect atmospheric flight.
Martian dust storms... swirling clouds of the gas giants with those storms running around...
Topography!!! Mountains, rivers, hills and valeys!
Real water... that your ship can sink in... that would freeze in the winter and thaw in the summer.
Support for other vehicle types, other then space ships. Everything that I've seen so far has the functionality of a space ship. From different MFD's to the HUD. Although people have built rovers and stuff, the propulsion behaves like a rocket engine
Granted, a lot of what I suggested would decrease performance by a lot... but hey, it's not like it's not possible. You can implement a few tricks to increase performance as well as you have to take into account that by the time new orbiter gets released... well, let me just put it this way: Who's gonna fly on a P3 anymore, right?
Given that some addons these days are so graphically complex that even modern computers are struggling with the DX7.