Actually diving time is irrelevent and could be twice as long. The American boats have radar. I never crash dive at all. Too much chance of leaving ahead emergency and eating up my fuel supply, and I'm out of sight before they're five miles away as it is.
The superior technology on the American boats makes you rethink everything you thought you knew about submarines from working a U-Boat. The balance of EVERYTHING is changed, and that is part of the fun of learning the two different boats.
I submit that the differences in the games reflects analogous differences in the operating procedures of U-Boats and Fleet Boats and that those differences should be preserved in that spirit (other than things you want to change, like the keyboard command layout. I'm not contradicting myself here even though I am.:rotfl

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For instance the different locations for the TDC reflect the command structure of the two submarines, and the inherent difference between the two TDC's. Using the TDC while you are looking through the periscope is more realistic anyway, especially if you are using the stock game.
All those torpedo spread angle lines, ship silhouettes and velocity vectors are completely unrealistic. When you set the TDC at the periscope you aren't tempted to take unfair advantage. Load up Trigger Maru and see what a targeting plot SHOULD look like.
So I would say learn SH4 first, then start making changes to suit. I think you'll find that especially in moving the TDC controls it would just be a lot of wasted effort. Just gentle suggestions from the peanut gallery.