First a recap of how the current system works:
WASD changes horizontal velocity of the ship on a plane.
Q and E change the vertical velocity in regard to said plane.
Mouse rotates the ship on two axes, with ctrl you can rotate it on the third
Shift brakes
To move, ship requires thrusters
To rotate, nothing is needed
There is a relatively low speed limit independent of ship dimensions, even in space
Brakes stop the ship immediately
Nothing is required to rotate
Vertical movement is dependent on the same thrusters as horizontal movement
Rotation is as fast for all ships meaning large behemots can rotate ridiculously fast
Speed is limited in space, which is unrealistic and somewhat annoying
Make current thrusters "main thrusters", which can only accelerate the ship forward, make them more powerful than now.
Add directional thrusters with lower power, that allow movement in all direction, but are less powerful than main thrusters. They are also responsible for rotation
Add brake block that is responsible for braking. Without it, braking is slow or impossible(but you still can turn around and thrust the other way around)
Remove the speed limit OR
If it's dictated by the lagginess resulting from sector loading, make it dependent on amount of thrusters and mass of the ship
Remove the slowdown effect in space, make it dependent on atmosphere above planets.
Add gravity affecting ships above planets
Add a togglable stabilizer module which can keep the ship horizontal relative to the surface of a planet and perhaps also asteroids. It can also counter planet gravity (using directional thrusters)
Make Q and E roll the ship and Shift/Space move it up/down. This should be more intuitive since that's how controls work in most games.
Make entering planet atmosphere at high velocity damage the ship slightly (although in reality it'd be more like hitting concrete at high enough speeds)
More intuitive controls
"dead" ships will no longer be able to rotate
Movement above planets will be much more intuitive
Disabling main thrusters won't immediatelly immobilize the ship
Ships will move more like one would expect them to - accelerate once and they will keep flying (at least in space), making space travel much more comfortable
With stabilizers disabled, ships will naturally fall to the surface of a planet, making landing much easier
Gigantic motherships will no longer rotate as fast and they won't accelerate/brake as easily (at least not without gigantic amount of thrusters of all kinds)
Ships will require more different blocks to achieve the same level of maneuverability, potentially confusing some players
Current designs will no longer function as expected