The central flaws of wartime landing craft

What were the major weaknesses of wartime landing craft?

They were uncomfortable and poor sea boats, with a narrow ability to operate safely and effectively in rough water.

Discomfort and poor rough-water performance were the principal flaws. The continuing effort to improve amphibious vehicles for harsher sea states shows that the problem persisted long after the war. A craft optimized to reach a beach still has to keep its crew and embarked troops effective before it gets there. Seakeeping directly limited combat usefulness.