The most obvious difference are the graphics. Port Royale 2 use the well known iso-view, diagonal from above, fixed camera angle and an outdated, because very low resolution.
Port Royale 3 is based on the same engine as Patrician IV: town view and naval battles are in 3D, the camera can be moved freely. The graphics are up to date.
You will recognize the sea map, it has been updated too. A notable feature are the towns, every one of the 60 towns have their own layout.
Only little changes have been done to goods and ships.
Realy new are the two campaigns, these were not available in Port Royale 2. Missing campaigns have often been criticised in Patrician IV. In Port Royale 3 two campaigns are available, one for the peaceloving trader and another one for adventurers that like to fight with their ships.
The multiplayer is another new feature: with up to four players you can compete against each other – no co-op like in Patrician IV.
One unpopular feature of Port Royale 2 is missing – the fencing!