That's why I suggested finding a new use for it. Why not put a 2nd one in Balamb and make it sort of a starting point on the world map? Then move the big ship to York and give it the option to transport to Belle Island rather then Balamb.
York is a port town anyways wouldn't it make more sense having the ship at a dock there then randomly south of Graal City? Then in place of the ship there could be a narrow bridge from the main land across to the DW entrance.
It's just and Idea. I agree it's a landmark and would be both a waste and a shame to get rid of it.