Implementing gravity in space would be pointless, since you're typically so far from any significant gravity wells.
Assuming you're sub-orbital (you mentioned mountains and cities) also poses some challenges, since FS2 doesn't really use newtonian physics. An easy hack would be to apply some negative value to the Y-coordinate velocity (in world space, not relative to the ship).
This would make flying a little odd: since conventional aircraft have wings that provide lift, and FS2 craft just have the big thrusters at the back pointing through the Z-axis, you'd need to fly up at an angle to go in a straight line.