I have played this game since day one and have come to the unequivocal conclusion that the Merchant Alliance is Evil. Hear me out... it is primarily their use of pirates and some of the goods they request.
First off their uses of pirates, why? With the gold hoarders you can understand why. They are the only ones crazy enough to brave skeletons, other pirates, are willing to risk it all for monetary gain, and go to obscure islands to dig up an X. Same with the Order of Souls the use of pirates is also understandable. The order is using disposable assets (pirates) to thin the ranks of skeletons and as far as I can tell probably do not have a large network or resources to field their own fleet. And again, pirates are willing to kill and brave the dangers for monetary gain.
This brings us to Merchants Alliance. Why would merchants need pirates to run missions for them. They clearly have the resources to field their own fleet and likely have merchant fleets somewhere out there? While we don't see them on the seas I think it is a fair assumption they have them...they are merchants after all. Additionally, there should be an inherent distrust of pirates as historically they are the ones giving the merchants grief and pillaging their stuff. Why would they trust them? Additionally, one has only to look at some of the wares they request which raises some serious questions....gunpowder barrels and snakes. What possible use could merchants have for gunpowder barrels? They are, at least in this game, used for mayhem and destruction. And they seem to be stockpiling them. Perhaps for their MIA merchant fleets. As for snakes. As far as I can tell the only thing they are good for is their venom. I have been a victim of their toxicity on more then on occasion. Sure these are only two of the things that they request and you can point out that they also ask for chickens and pigs. While this is true, it is quite possible the chickens and pigs are just red herrings for their true aim.... I can only assume they are building up for something big.
(just something I thought up while getting bit by a snake while its pitch black out....why does this freaking merchant want this thing anyway. Thoughts?)