Nearly all the things you guys mentioned that are missing from SH3 have been fixed or added in the Grey wolves expansion mod (known as GWX2.0) It easily doubles the content of the game, Install it and you will wonder how you ever played SH3 with out it.

1) Many MANY more ship and aircraft types
2) liegh lights and rocket attacks added to allied aircraft,
3) Type14 resupply boats now operational, Axis and allied submarines on patrol.
4) the campaign is much more hisrorically accurate (shipping lanes and convoy routes etc) Loads of traffic and docked ships in feindly and enemy ports.
6) More Flotillas added, you can now start a career in Jakarta or Penyang as a monsun boat (type IXD2) in the east. or take a type II boat in Conzantina in the black sea.
5) Tons of Graphical glitches and bugs fixed.

You can down load it from www.subsim.com, Trust me, the subsim community poured their hearts and souls in to this mod and It will knock your socks off.