Way back in the day Hump and I worked on a DDay type map.
Actually it was his idea, and he employed me to create the landing crafts.
The way I did it was as follows:
I made a DDay style landing craft. The craft started out to sea a bit in water over your head. At the beginning of the game everyone spawned above the craft. I had to "drop" the players into the boat because being the craft was an entity it had to have a second to become solid or the player would fall right through it right at the start. The entire craft was a func_train that simply started out at sea and went in towards the beach. Next problem was the door swinging down to let the troops out. Unfortunately you can't have a fun_train, and a rotating entity as the same object. To combat this, as soon as the craft came to a stop I continued the swinging door's func_train and shot it down thought the sea floor to make it disappear. When the craft came to a halt there was an identical door already sitting there waiting for it. So with the original door gone down through the sea floor, and the new door in it's place, I could apply a rotation to the new door to make it swing down and open for the troops to come storming out of. The problem was, now you had this door sitting in the middle of the water close to the beach. This could look odd from shore. From inside the craft it looked absolutely perfect. Unless you were REALLY REALLY looking for it, you couldn't even tell the doors were switched as the craft came to a halt. And in that particular map the Germans spawned far enough away from the beach they couldn't see the little door sitting out there alone in the water.
Granted this type of thing take a lot of time and patience to get perfect. And after all that work the map was never released. But that's the price you pay for perfection. It looked pretty darn cool watching it work. At the time I didn't know how to spawn players with gear, or even if it was possible. Gear falling through the boat to the sea floor on spawn was another issue I had to deal with. In the end I got it working perfectly, but it never came to anything.
Good luck with this map. I really hope you go for the animated landing craft approach. That would rock!