I personally wouldn't call it a waste of time and money and certainly wouldn't really expect a 500 year old ship that sunk in 1545 to remain intact underwater for a long period of time. Its remarkable most of its superstructure is still intact. A very rare occasion it is to find a perfectly preserved ship made out of wood.
The fact they managed to salvage this 400 years later, but cannot salvage the titanic (built in 1912) without destroying it. Shows the level of engineering involved in building the Mary Rose.
The reason we don’t touch the titanic is because it is not that old and historic compared to the Mary rose. Historians and anthropologists don’t really give a crap about the titanic compared to the Mary rose. We have so much to learn about how people lived back then, especially during battle, which is when this ship was used. This ship is a piece of history. The titanic is not. We just romanticize it.
