In Space Engineers, you can build your own ship from scratch, you decide every little aspect of its size, weaponry, speed, maneuverability, storage size etc. (reminds me of FF OBT crafting)
In NMS, you either buy one or search for a crashed one and repair it, but they will all fly the same, and you cannot crash it into anything, or destroy anything with it aside from pirate fighters and asteroids.
This alone is enough to side with SE.