Many of the things you bring up are addressed in mods. yes, I know it would be better if they weren't necessary, but they are out there. From what I've heard, with RuB, you take planes on routinely and you'll end up a hulk at the bottom of the ocean before long.
I'm wondering if you're patched to 1.4b. After the patch, it will ask you what you want your 'default action' to be, whether to dive, engage or do nothing..this would partially automate your process.
Mods also address the merchant guns, especially deadly the later the war goes.
One of the MODs (SHC 1.43 I believe? Or is it something else?) does update the map as you ask, showing the progress of the war.
Can't speak to the FAT. I dont' think that that can be modded.
As to why the crew reports every ship, it was never that granular to different reactions for enemy, friendly or neutral vessels. Why? I don't know. Think of it as I do, the crew will likely notify you of a ship before knowing whose it is. Then you can be told it's German and go back to the sleep they woke you from
Keep on thinking, it's healthy.