None of the mods affects U-Boat playability yet. The environmental mods are affecting that. But we still have the U-Boat on rails, so they aren't quite doing what they do for the Fleet Boats. I don't know how you get historical enemy shipping when the scenario is hypothetical. I'm in the minority in that I don't have a problem with hypothetical situations.
But for the U-Boat, we're at ground zero! The game is this good and we haven't even begun to see what's possible! If we can get the evil

Kpt. Lehmann healthy again, there's a chest of goodies (toyz!) here that would get any pirate excited.
One small annoyance has been the incomplete separation of U-Boat and Fleet Boat has made Trigger Maru affect U-Boats badly, and I'm afraid it might be the other way around. It's too bad that they are not totally separated.
I would suggest a way to make that happen, even if the game can't be brought to heel is a modification of the main menu that would take advantage of a MultiSH4 dual setup for U-Boats and Fleet Boats. That would mean two JSGME setups and other messy details, such as an installation script that would assemble this frankenstein monster properly for the player, and may mean some fancy footwork in the menu coding bordering on license violation. Cooperation with the devs would be absolutely essential to avoid any of that becoming an issue. If Ubi feels they've been betrayed by their biggest supporters, we can kiss future sub sims goodbye.
Sometimes I wish I were a modder, but I have a life and don't have the time to learn. I'm bright enough not to wish I didn't have a life!
@Penelope: I forgot! You can load up my
Trigger Maru keyboard layout, featuring shift-i for someofficer identify target. It's very similar to SH3.