Great game, with *one* major flaw; the issues everybody else is pointing to all stem from the fact that there's no middle or end game.
After getting the first two upgrades, with their extremely rapid rate of cargo and combat increases (which is perfectly done) the game starts repeating itself. You run on a treadmill, doing the exact same thing 4 more times, occasionally attacking a town (which is no different than the sea battles, aside from the plot-bar), and then have a final battle which is identical.
Contrast to "Rebuild II" - where after a bit, you start having random events occurring, all of which affect the game's outcome.
Have the random encounters be more threatening - I only got ambushed once throughout the entire game (most players probably don't even realize that you can be ambushed) - but have the ports in the area sell FAR more profitable items.
Add plot points to the trading itself. Sub-missions.
Add special abilities to the ships - so that I can choose a strategic mix, rather than simply a combination of the most expensive ships.
Also, there's the money problem; at first I was forced to trade, which was brilliant, but eventually I became so rich it was ridiculous. 5 minutes of grinding can net you a fortune. A possible solution is to make the pirates time-sensitive, getting tougher as time goes on, ergo leaving you with a losing game if you choose the wrong strategy.
Nonetheless, it was an excellent game with a lot of great work; as others have said, this deserves a sequel!