I've been running S&S for the last year and we'll be finishing in this Tuesday. From what I've seen...
To get the bad stuff out of the way, I would like to first say the naval combat system isn't very exciting or engaging, or realistic. For the most part it's your ship's captain making skill checks against the enemy's captain, and the rest of the group can...make assists, or fire seige engines that for the most part are useless--if you do enough damage to have any effect, it means the enemy ship is worth significantly less, or you sink it and miss out on a literal boatload of treasure. I would suggest using the homebrew ship combat here http://paizo.com/threads/rzs2p54b?Naval-Combat-For-a-Whole-Party#1 or get the Fire as she Bears book, which I hear has a great ship combat system, and a better system for ships in general.
Parts of the adventure path, particularly in the beginning, can be quite deadly. This creates a problem in the first module, as for your first level and a half you're on a ship with a clearly defined number of people all with names and (for the most part) stats already given, so it's nearly impossible to explain introducing a new character. After that however, a little flexibility can make introducing a new character fluid and easy--but you'll need to give them a backstory for why they hate the rest of the party's previous captain (though his tendency to have mutinous crews doesn't make that too difficult--we know of at least two successful mutinies against him).
There are also a few parts that feel railroaded, especially the first module which seems to drag on forever in an effort to drive into your players a hatred for their evil captain. Unfortunately what it really does (as written) is to develop a hatred of the first mate, which is important, but the captain himself is mostly absent for the module--literally three lines of dialogue and he hands it over to the first mate. I would highly suggest including him some more with some cruel behaviors (look in installment 5 for inspiration, he is a sick, evil bastard). There are a few other parts (part 4 particularly) that feel somewhat railroaded if the GM doesn't take some steps to make it feel more natural.
It is not all like this however--part 2 (except the very beginning that gets you on your ship) is a wonderful sandbox is run correctly, filled with opportunities for some gool ol' piracy. Use the "random encounters" here to create some higher level opportunities at higher level and you can eliminate some of the railroad feeling later on. I personally upgraded the pirate hunter and ghost ship battles and put them in modules 4 and 5 respectively.
This AP also has many wonderful RP opportunities and great benefits for making skilled and/or clever characters as opposed to standard "bash door, kill monster, take treasure" types. It's filled with colorful NPCs that feel real and relatable, enough so that one of my players' characters started a relationship with one and they're planning to get married at the end of the AP. Another character is already married somewhat against her will, but that's another story altogether (though also shows the advantages of not straight-up murder style).
All in all my players loved this AP without too much need for modification on my part, but you do have to make sure to read ahead--I would suggest skimming through the entire adventure path before running the first module. It'll let you set up alot of hooks for later that your players will love, or love to hate.