Crew abilities arent a problem. Its player abiliites that are the heckler. I had an idea last night on something that *might* work, but i doubt it. Its one of those things that are a shot in the dark, probably wont work, but worth trying anyway incase your hunch is wrong.
That hunch, is *MAYBE* (big maybe) control of assest is being dicated by the sub. Theres a "special abilities" controller (or name similar to that) in a sub sim file. Now, this controller has always been there, but the thing is, the proprties of said controller isnt currently readable by S3D. If i was a hex editing genius i could tell you whats in there, but i cant. So the shot in the dark thought is, maybe theres a boolean switch in this controller that was added in the german uboats, but not in the US subs. The sim files weren't touched by the uboat addon for fleetboats, so its entirely conceivable.
IN sum, try exporting the properites of this controller from the german sub, into a fleetboat, and see what happends.
Really far fetched idea i know. I hate mentioning it cause it sounds really stupid, but i experiment with stupid crap like this all the time. Sometimes i get lucky. (most of the time i dont
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edit: Dont forget to set "is tactical" for US airbases to true in the air layer, and allow some player ablitlies at the lowest possible player rank so you can experiment.