A major problem that I had with SH3 is that after weeks of play the game would suddenly forget the savegame file and not be able to find it. Inquiries revealed that you could not save the game if any ship appeared on any sensor, if you were not surfaced, if you were within a certain distance from land, if you were wearing any item of blue clothing or saving on any day of the week containing a "y." OK, the last two I made up.
The SH4 engine has totally solved those problems and all my saves over an 8-month period in all kinds of random conditions have been fine.
I'm not sure if that is what you are after, but you have to admit that satisfaction in the game is very dependent on the ability to play a career successfully.
Crew management has also been changed with watch changes automatic and each compartment containing three watches. You can still move crew members among available slots.