Rafts ... for one they don't bug you as contacts anymore. They still make stupid screeching sounds but that's about all they do. As for the airmen, patch 1.3 fixed that up REALLY nice. Most aviators pop red flares that are visible to you from 7-8km. The crew still is blind as a bat when it comes to spotting them but you can easily manuver the sub to the flare.
Crashes are a thing of the past. Most were fixed in either 1.3 or Jace11's tiny mod (which was included in countless other major mods).
The stations themselves aren't as interactive as in SH3. The radar and sonar stations are much more useful in 1.3 than they were in 1.0 however.
And the sound... what sound?
EDIT: Damn, Duci beat me to it. Fast skipper
Anyway... there's still a little naggin issue with crew's eyes and the bow planes but they're minor and usually go away on their own.