To make this as unspoilery as possible, the decision you make at the end of the campaign has very little effect on what happens postgame. What differs based on your choice is the location of Jin's new home (the actual dwelling and its contents are exactly the same either way) and the color scheme you receive for the ghost armor.
If you
, you get a white color scheme for the ghost armor. If you
, you get a red color scheme. That's the only real significant motivator for the choice to be made.