I hate to say this, because it has some of the coolest technology in the game, but the part with the pirates/rusty shipyard/cruise ship feels totally out of place and tacked onto the game.
The water mechanics are incredible, and the devs at Naughty Dog are amazing, but the whole thing felt more like a tech demo inserted into the game at the most random moment. In fact, it kind of feels like DLC because the only main character from the rest of the plot is Drake.
Considering the plot of the game picks up right after where Drake was kidnapped (back in Yemen), it feels like it could have been completely cut and nothing would have been missing from the plot. Instead of being kidnapped by the pirate boss, Drake escapes and goes to Elena's little hotel room. Boom. And we're back on track with the main adventure of the game.
I actually enjoyed the shipyard and cruise ship setpieces just because it was all visually so cool and, like I said, I really liked the water mechanics. And the idea of pirates tooling around in this massive luxury cruiseliner is cool. But, storywise (to channel Sully from earlier in the game) "I'm losing the plot here, Nate."
Who is this pirate boss? Why is he working with Talbot and Marlowe? Oh, who cares about any of that because he's killed off quickly.
Honestly, I really imagine that Naughty Dog had developed the water technology stuff and wanted to get into a game so they just Team Ramrod'ed it into this one where ever they could.