Two things I'd like to comment on here...
1. The issue about crashing while following a plotted course into a harbor and the refit options popping up, this happened to me as well. When the initial refit/postpone/dock screen pops up your sub will continue straight ahead at whatever speed you've set it for and Time compression will remain active. I entered PH following a neatly plotted course on about 1000x time compression and my sub did not stop at the final waypoint but instead continued full steam ahead to ultimately plow into an American destroyer sinking us both. So I know the frustration, from that point on I always take the last few miles of approach slowly.
2. As to crapgame's irritation with micro management...I've had issues with battlestations etc...but this game isn't really that micro management heavy(Try playing some of the total war series), afterall its a simulation not an arcade style game.