I spent considerable time to complete this game, because as a mobile game I play it on and off and never quite pay enough attention. The good thing of a mobile game is that it eats up time when you're bored and have absolutely nothing better to do, like waiting for a bus. I will detail a guide on everything about this game (since no one really have one good enough yet, or even one at all).
First off: ships - all the ships, their stats, their in-game performance, which one to choose, to upgrade and to buy first.
For early game I used The Wanderer and did missions until I can buy the Fearless, which I used throughout mid and late game. For end game I used The Citadel (later The Untamed) as my core combat vessel, and switch to Brisk Fortune (with Mercury skin for +5% Speed) to get 100% in race, escort and package delivery missions.
Gunboats hold 1 Spider shot at maximum, start with none every battle and has to be earned.
UPDATE - June 12th 2015: Understandably, Serpent has no stat boost in the recent upgrade. I would like to see a little more love for this little dinghy though.
As for ship progression, I used the Wanderer for most of the early game and skipped the Brig-class to get myself a Frigate.
Schooners can have 2 Spider shots maximum, also start with none.
UPDATE - June 12th 2015: The Wanderer received an extra Defence stat, making it a 3 in Defence.
The HMS Drake does have a stat-boosting skin (Spanish, +5% Speed), which might be desirable for pirates having a need for a faster ship yet doesn't have enough bounty to buy the Brisk Fortune, the fastest ship in the game.
UPDATE - June 12th 2015: HMS Drake received an extra Defence stat, making it a 3 in Defence.
The Jack Snipe
In fact, skip all the Brigs and save up for the slightly more expensive but vastly more powerful Frigate.
Brigs have 3 Spidershots maximum, start with none.
UPDATE - June 12th 2015: Oddly, the only connection ship-wise with AC4 received no love from the dev team, and came out of the update with no stat gain.
Citadel no longer matters as Untamed is now the end-game ship of choice, so skip it, as my readers concurred.
I used Citadel for most of my late game until I get my first 1.500.000 and the end-game Man O' War to strive for 100% completion of everything. This is a beautiful ship...until the update, of course. My bad people, I've been playing for too long!
Frigates can have a maximum of 4 Spider shots, start with none.
UPDATE - June 12th 2015: The Citadel received an extra Power stat, making it a 5 in Power.
UPDATE - June 12th 2015: The Riptide received an extra Speed stat, making it a 4 in Speed. Still not really worth it.
But the most important thing is probably the fact that it is a Schooner-class, so the thing glides and handle like a dream. Even without the Minesweeper perk (decrease 75% mines in escort missions), Brisk Schooner can glide in between and around mine fields like an excited sparrow.
Brisk Schooner is how you glide through the highest level missions in racing, escort and package delivery. With some damage perk, it can also be how you quickly earn 100% in the earlier levels just because it's so darn fast.
Remember that this is an end-game ship, and is used for full completion once you've had a lot of money, not campaign battles!
UPDATE - June 12th 2015: The Brisk Fortune received an extra Speed stat, making it a maximum 6 in Speed. Nyoom.
Much as my memories deceive me, skip Citadel and get this ship. Like Citadel, it has 4 slots for Spider-shots.
UPDATE - June 12th 2015: The Wanderer received an extra Defence stat, making it a 5 in Defence.
You will find yourself avoiding Race missions from Nassau onwards using ships as large as Frigate-class and above, especially if you strive for 100% completion, as the Frigates and Man'o'Wars while great at handling is still very bulky and Speed stat is simply not enough for close-quarters maneuvers round the minefield.
With the new update, Spider shot can be used to skip the Fruit-Ninja-combat as well, so it is even more important nowadays. A large Spider shot reservoir is useful especially in Survival missions and Fort campaigns.
High Speed doesn't have any effect on dodging mid-combat, while a better Defence does help combat a lot, so yes, The Untamed is currently my end-game ship for fighting and looting in high level maps.
All Man o' War have a 4 Spider shot maximum, but unlike Frigates, Man o' War starts the battle with 1 Spider shot already equipped.
UPDATE - June 12th 2015: The Untamed received an extra Speed stat, making it a 5 in Speed. Very well rounded near-end-game ship.
Good stats is nice but it has to fit the ship. Also, everything is overpriced - the Poseidon skin is 500.000 and doesn't even have any effect (not to mention very stupid-looking, unless you are REALLY into blue). I bought everything out of spite and because I reached money cap anyway. (The max-gold-in-30-minutes has been patched. Sad face)
UPDATE - June 12th 2015: The Goliath received an extra Speed stat, making it a 6 in Speed. I see it as an useful replacement for Brisk Fortune in campaign missions that requires some chasing and fighting at the same time. Goliath is still not viable as a racer however - far too bulky and the massive sails block most of your view regardless of camera position.
Don't buy this thing, just don't - unless you are like me who reached cap and buy everything for the sake of shopping.
I do have a weakness for purple, however. Nice skin.
UPDATE - June 12th 2015: The Abyss received an extra Defence stat, making it a 5 in Defence. It's horribly sad to see that just for double price you get one more Power and three times the Speed. The buff that almost feels like a nerf.
The Devil's Due
As usual, the skins are ugly and mainly useless, save for the Temple-unlocked skin, which I am gunning (heheh) for. Since I'm writing this as part of my June 12th 2015 update, there is no change (for now).
I highly recommend The Devil's Due, even for the damage alone. 5 Defence is plenty even for the hardest of campaign missions, and 6 Power can be a good way to crush the harder Survival missions if you haven't had the time to grind for the Double Damage legendary perk yet. When you have both Double Damage and The Devil's Due maxed-out cannons though, the seas will shudder.
Ugly skins though oh my god (except for Grim Reaper, all-black is always cool).
UPDATE - November 22nd 2014: I changed the Fearless and Citadel parts thanks to Jim and a few other readers' suggestions - thanks to all for the comments and info! As a player from the earliest days, it's hard to remember something you purchased a long time back.
As for the Phoenix (premium real-money purchase) and the Dragon (iOS ship), I'm sorry to not be of much help. I don't pay for extra money and ships, and I use an Android, unlike my cousins :( sorry folks
I'm writing up on the Perks, which should come out some time in next week or so, now that I can see an end to my work. Thanks for the attention and the wait!
UPDATE - June 12th 2015: As requested, I added the new class (with only one ship released for now) - The Ship of The Line class, with the ship Devil's Due as its first ship. Impressive ship, despite the bulky looks!
I have also noted that some ships now have a new set of skins, the Temple skin. All Temple skins give an extra 5% to Power, and requires the completion of Temple missions in campaign.
After a recent update, most ships has a single extra level for its most notable perk (the already speedy Brisk Fortune gets an extra Speed stat, for example). The level 6 upgrade cost 80,000 gold, but an impressive 5000 resource, accounting to approximately 50% of the resource cap.
Sometimes ships have Spider Shot right at the beginning of the fight, sometimes they don't - I'm not sure whether it is campaign-specific or a weird bug. Despite its relative age for a mobile game AC4: Pirates is still bug ridden.
Oh and the gold thing is patched already :(
I'm too lazy to reupload all the pictures, but except for those upgrades things are largely the same (for ships).