My main complaint with the flight model in SC is that the thruster input is purely digital and over zealous...where as in Elite, it's analogue and extremely controllable. Makes all the difference when flying with a HOTAS for me. SC was designed at source to be flown via M/KB...Elite, not so much.
It isnt so much that the input is digital, it is just how it fundamentally works that makes it awkward (at least in coupled mode). If you set your HOTAS to 1/4 throttle, it sets the target speed for the ship and SC will go at 100% thrust until your ship reaches the speed. You aren't setting thrust to 1/4, you are setting your target speed.
If you fly decoupled and you set your HOTAS to 1/4, now it is setting the thrusters to thrust at 1/4 power. I pretty much fly decoupled 100% of the time at it is much more natural. Going back to coupled and the throttle response is a bad experience for me.
SC isn't so good for keyboard users. Mouse is fine.