Don't let appearances deceive you - you're looking at the former flagship of the Assassin navy - if perhaps a little past its prime.
The design was incredibly innovative for its time - the ship was light, fast, and could carry a surprising amount of artillery for its size. It would be decades before there were schooners that could match the Aquila's speed. Of course, there were some disadvantages to the design - namely that the ship handling was very touchy and required an experienced crew. That meant the Aquila was under-utilized until the Assassins hired someone who would be able to use the ship to its full potential - Robert Faulkner.
In 1754, the Aquila followed a Templar ship into a storm and was lost with all hands aboard - or so we wanted the Templars to think. In reality, it sustained only minor damage, was refitted, and became the Assassins' secret weapon - staying out of major harbours, using its speed and the element of surprise to harass ships on Templar business. The Aquila took on mythical qualities - it was whispered about in ports along the eastern seaboard as the "Ghost of the North Seas" - a pirate vessel crewed by ghosts that could appear and disappear into a sudden fog. (This reputation was due to Faulkner's uncommon skill, and the superstitious nature of most sailors, who loved a ghost story and all wanted to marry a mermaid.)
Eventually the Templars cottoned on to what had happened - but it did take them more than a decade. (They weren't the sharpest tools, let's say, in a box full of spoons.) In 1768, the ship was caught in a trap by 3 British frigates. The Aquila was able to limp away from the battle, but ran aground in shallow water. The British left it for lost. Robert Faulkner survived the battle, and had the ship towed back to a private bay near Boston, where it - and Faulkner - slowly deteriorated.
That is, until Connor found them both.