Wolfpacks, many more flotillas, the XXXIII (or something like that... it was a small craft like the II, meant to replace it), MORE SHIPS, ability, and a more thorough betatesting, as well as a more friendly interface (to me, the vanilla save-system is among the top priorities)! The learning curve and all is fantastic, so nothing needed there as far as I care...
Oh, and BETTER (and MORE) HARBOURS. The stock harbour is just gruesome! Like Key West. Absolutely horrible.