The problem is the deck height above the water surface. The plane wants to land on the surface, and not on the deck. The previous work around was a ship model that was a flat deck at the surface of the sea for landing and take off (only visible at close range), but appeared normally once the LOD resolution dropped when you got farther away. A bit jarring to see, but it worked.
House Hobbit found a way to do air starts down at ship heights for some of his missions to simulate catapult launches.
I've always wondered it we couldn't just use specialty aircraft models where the contact points offsets are such that they match the distance of the deck above the sea surface. The problem with that comes when the plane comes to a stop, and the ship keeps on moving out from under it.