ORIGINAL: invaderzim
The problem is when your ships run out of fuel. They slow down to impulse speed which is about the same speed as the planet. They are so slow that sometimes they can't catch the planet, so they can't refuel. You can do some fancy micro with a resupply ship since it can come to a dead stop, but this very annoying.
Not true. All my experiences show otherwise. Ships ordered to move to a planet/spaceport, refuel at a planet/spaceport pick up the destination's momentum, so the distance they have to travel is the exact distance there is between the ship and station/planet at the exact moment you give the order.
So they travel on a straight line, although this line moves with the planet as it orbits its sun.
And on the straight line the ships travel with their base speed(the one shown in the unit overview panel).
The only time I had to scrap a ship because of a similar reason was when I made a fat, slow colony ship which ran out of fuel before reaching its destination and it stopped completely (or moved so slowly that I didn't see it 4x speed).

