Reality Subtext: The MacGuffin in this game is, for all intents and purposes, magical NSA, with the Templars believing that it would help bring justice and order to the world. Which is ironic, since the PRISM scandal broke when this game was well into development.
El Tiburon was apparently more prominent in early versions, with him and Edward having a one-sided Hopeless Boss Fight even, as per Darby McDevitt which is what Edward refers to at the end in the game.
According to Darby McDevitt Edward was originally going to end up witnessing Mary Read and Anne Bonny fighting off the British Navy. In the final game, Edward witnesses their sentencing and their pleading their bellies and eventually Mary's death.
It could have been Elite but with Pirates (and, of course, some Assassin/Templar stuff). Unfortunately the fact there are only five commodities which always sell for the same price and your ability to sell them and buy ship upgrades without going anywhere near a port spoil this.
Remember the awesome Homestead sidequests in ACIII that gave the game a surprisingly personable feel? Well, that's gone. Instead of building an awesome pirate hideout - which is perfectly possible, as a base one is given to you pretty early on - you just buy different shops you want.
The original ideas for DLC was to an Alternate Universe "Devils of the Caribbean"(after the cheesy in-game trailer) that would feature the Pirate tropes the game makes fun of - bad accents, parrots, krakens - similar to the "Tyranny of King Washington" DLC. Likewise before doing an Adewale based "Freedom Cry", they considered making DLC for "James Kidd/Mary Read".