Hi,
Well you named off a few of my favorites already....
1) PTO and U.S. Subs!

2) 2. People walking on and doing stuff on the decks of ships
3) Harbor Traffic
4) Well done realistic TDC (although a few bugs right now)
4) New Crew Management
5) New Damage Control will be good I think when a few of it's kinks get worked out
6) A fairly good portion of the game/sim is made so that modding is possible
7) Good graphics without needing to high of system specs, although desperately in need of higher resolutions and anti-aliasing(blocky, jaggy, and shimmering all over the place)
8) I dig the post processing effects
Cheers