In my view the game can be improved in three broad areas:
1. technical simulation
2. graphical appearance
3. content
Simulation... big improvements needed, IMO right now it doesn't qualify as a sim. Rudder effect tied to engine RPM instead of surface speed? Stuff like this needs to be fixed pronto. Of course, more complex refinements need to be made as well. Ship AI is a major thing, they must not blindly run into you. Introduce training missions explaining the harbour rules, speed limits, right-of-way, navigation lights and buoys, etc. Rest of missions should then take those into account. More controls on the bridge - lights, comms equipment, added radar functionality, wall charts, anchor cables, etc. I try to only use first person and would appreciate several crew on each ship (depending on size), with visible avatars, between which I can switch - so I keep one on the bridge and walk the others to the bridge wings, bollards, wherever I need them.
Graphics wise the textures and interiors can use a big improvement. Interiors should look more authentic, together with instrument functionality mentioned above. Other parts of the ships need more texture/lighting details, and non-player ships like the yachts and sailboats are let down by low-res textures. Introduce nationality flags?
Content-wise... every environment should have its own water taxi, tug boat, ferry/tourist/passenger vessel and large cargo/tanker ship, all playable. Followed by half a dozen non-playable cargo/fishing vessels to make up the traffic. These should be ficticious (no license is needed) and have several texture schemes each so there's more visual variety. This content should be added retrospectively for the existing environments, which would fix NY and Cisco Bay being populated only by Euro ships. Perhaps in a 2010 version such environment packages could be marketed separately, i.e. you purchase the base game and you're allowed to download one environment package for it, after that the others cost extra? There's enough environments for now although for balance purposes maybe add one from Asia - perhaps Singapore?
Lastly I'd like more sound effects and ambience, circling seagulls, tricks like that to make the places feel more 'alive' even if there's no people visible.