This is the mission that takes place in shallow water, right? That sometimes plays a role since the ship is still somewhat out of the water.
As for the long transit times, there's a lot of things you can do to keep yourself busy while still in earshot of the game. Half the time I'll take a break and just watch the U-Boat cut through the waves. I never get tired of the effects in this game. Or do some cleaning etc. I usually get more done around the house when I'm playing this game than not playing.
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