What I'd like to see is actually having a destination to pick up the items, particularly the animals. Explosive barrels are fine because they're plentiful in forts but animals just feel random to find and frustrating. I've looked on islands with reported animals, particularly chickens supposedly being on Thieves Haven, but I have never seen a chicken there once. Some consistency would go a long way in improving its feeling.
Second, please make it a passive voyage, similar to a message in a bottle, rather than active and therefore, taking up the slot of an active voyage (such as through the Gold Hoarders). That simple change would go a long way in just happening upon the right items while out voyaging for something else. I had a message in a bottle with a Merchant Alliance mission last night and it felt less tedious to find the items as I went along rather than be forced to go island to island not finding what I needed running around like a hapless chicken.
Third, please just give us an item on the ship to store resources such as coops. There's no two ways around it: getting coops from the shopkeep is just plain bad. Hoping to find a coop on an island isn't much better either. There are plenty of unused barrels on both ships, so having a universal coop would be fine. There's no reason they should be segregated by chicken/pig/snake anyway.
Lastly, remove the specific outpost to turn in the items for the current voyage. How annoying would it be if Gold Hoarders and the Order of Souls required you to turn in the chest to a specific outpost? For some reason, that stipulation is exclusive to the Merchant Alliance.
A potential idea to make the voyages more engaging instead of how it works now is to get the items ahead of time from the Merchant Alliance, instead of having the ability of selling the animals/explosive barrels, and deliver it to somewhere else. In other words, you get the items from the shopkeeper instead of the coops, load them up on the ship, and deliver it to a different outpost. Just an idea on that.
If ALL else fails, please greatly increase the payout for just selling items without a voyage. It is painful at present; I don't even think one receives credit for selling animals by themselves. This renders picking up animals out in the wild for sale entirely pointless. I would like to be able to have some incentive to actually acquire money for them instead of lost hopes and dreams and feeling like I just wasted all that time.
I love this game but man, right now, the Merchant Alliance is such a drain. Right now, I just despise it and hope that it either gets an improvement or a non-requirement from acquiring Pirate Legend in the full game.