Wish list
1. more ship types.. and showing if they are loaded or unloaded (height wise in water).. who'd waste a torpedo on an empty ship
2. Crew management... deffinately worth allowing the player to select what crew members go where on a watch cycle, and they remain on that watch cycle rotation unless they are exhausted / killed etc.. if you can train them then make sure you can put them where they will actually do some good.
3. ability to use electric motors on surface (might be good if u need to sneak close in to a beach at night to rescue special forces or spies) i like the sneaky factor
4. mission types... allow for subs to be used for recon / carrying vital supplies / dropping off spies / comando's etc etc... subs were used to get food / fuel to malta during WWII and some dropped off the odd shore raiding party.
5. release a cut down SDK which would allow the Mod community to further improve / add to the games playability, you only need look at the mods peeps have done for SH3 to realise there are alot of really good modders out there
above all make the game enjoyable!