Landing crafts are spent after the invasions. Transport remains. Also landing crafts like the ones used in Normandy are fragile structures with wood bottoms. Their only purpose were do a short travel from the transports to the beach.
A different thing would be the specialiced vessels that were used by the USA in the Pacific...that never saw the European coast.
It's like the amphibious armored vehicles that they started to use in the invasions after Guadalcanal (I think that they started to use them in tarawa, but I can be wrong). They were used only in the Pacific. That the reason for the disaster of the tanks sent to Omaha (from 30 launched, only 5 survided, the rest sunk during the travel).
My bigger concern is that operations like Overlord are difficult due the lack of supply sources. The port capacity basically left half of your invasion army in Basic supply, so no replacements and efectiveness recovery. That left those unis really prone to be destroyed in a counterattack. If you add the factor that you don't have control about what units will receive the supply from the ports (sometimes the front line ones, sometimes the rearguard ones) landing in Europe in force can be a leap of faith sometimes.
This said, I also agree that the ninja disembark tactic is a bit "creative".
Most landing craft used by the Allies in Europe could be broken down into two types. The assault landing craft are the ones most people are familiar with; the smaller craft with the ramp in front that lowered down. Most (but not all) of these were wrecked in the invasion. But the follow up troops and all the men that landed in the weeks after the invasion were primarily carried in LCILs (Landing Craft Infantry Large). My father-in-law served on one of these at D-Day. These ships were much larger, were not fragile and did not have wooden bottoms. They were also reused during Anvil. I have to think that landing craft in the game represent both types. So I would be quite happy if only half of landing craft are destroyed upon use, so long as the cost is increased to at least that of transports.
I agree with you that a player should be allowed to build mulberries at tremendous cost if/when he achieves a certain invasion tech level. This is not my idea either (I think it was Sillyflowers).
I think that the LCIL are covered by the transport capacity, in the end they are actual ships. The assault landing craft are the ones that are spent in-game.
Anyways, If I'm not wrong (and I can be) the bulk of the infantry that landed on the beaches moved directly from standard transports to the assault landing crafts. Also I remember that readed in some book the the USN had only 3 LCIL operative in Europe, and one got out of combat due repairs during overlord time.
I agree that LCILs are ships, but I don't believe they were generally used for transporting troops long distances. For example I don't believe they were used to transport US or Canadian troops from North America to Europe. They were specifically constructed for the purpose of landing troops onto beaches. I am more familiar with the DDay landings on the Canadian and UK beaches, so I can't say how many LCILs the US used. But I do know that far more than 3 were used by the Canadians and British. I have a photo of my father-in-laws LCIL at Juno beach and there are 3 or 4 LCILs lined up. His LCIL made several trips in the weeks after DDay, including ferrying US troops to Omaha and Utah beaches.