Takes time. I’m sure you’ve heard it before, and it’s entirely probable you guys already considered and decided against implementing ship travel this way, but hear me out!
Putting the player in a boat and travelling in real time between harbour cities would not only increase immersion by a significant margin, but would also work to remove that cheesy feeling you get when you pop off to get some cheaper food & supplies, and return in an instant, while defending a city from a Siege.
Hell! As part of a future DLC (which I will be instantly purchasing no matter what it contains ;) ) perhaps while being transported by boat, a small chance of a pirate boarding incident could occur! Or events where bros may get injured (e.g. weather events, pirate bombardment)