Most profitable trade routes

Solution 1:

As you progress with the trade routes other locations open up. They become more and more profitable as you continue to open more locations. The more profitable locations do require larger ships(more cargo space) like the Man o' War. These more profitable routes also take more time though.

For a list of better ship locations, names of other Trade Missions and tips check the link:Kenway Fleet Guide

Solution 2:

Bissau, Cape Verde
Giant Appetites – 3,400R
Meet the Tributes II – 3,400R

Cape Town, South Africa
Table Bay’s Luck – 5,000R
New Economic Hub – 5,200R

London, North West Europe
A New Cathedral – 3,800R
The Poet – 3,500R
The Great Plague – 3,500R

Galway, North West Europe
A Long Voyage – 3,200R

Gibraltar, Mediterranean Sea
Great Reputation I – 3,200R
Being Mad – 3,200R

Barcelona, Mediterranean Sea
Great Reputation II – 3,700R
The Catalans – 3,800R
The Smokers – 3,700R

Marseille, Mediterranean Sea
Great Reputation III – 5,200R
A New Medicine – 5,200R

Ref: http://www.tradeindetectives.com/blog/how-to-earn-the-most-money-in-kenways-fleet/

Solution 3:

I came across this issue mid game as well. Scrolling through all the missions and comparing them is a pain in the neck. So I made a spreadsheet ranking the best missions for each cargo size. Many of the missions that "perfectly" fit that cargo size are highlighted in the sheet.

Below are the top missions for each cargo size by return. Notice that many of them are smaller "loads" - they pay better than the larger ones. The "New Economic Hub" is the most profitable mission and only requires 30 cargo. It's worth noting that many missions have other rewards not reflected in the spreadsheet, and most need to be unlocked by doing other missions first.

• Cargo size 15:
  • Portugal: Do No Harm - 1700
  • Bay of Biscay: Sweet Broth - 1500
  • South Atlantic: Diplomacy III - 1300
• Cargo Size 20:
  • Portugal: Do No Harm - 1700
  • Bay of Biscay: A Sweet Journey - 1600
  • Bay of Biscay: Sweet Broth - 1500
• Cargo Size 25:
  • Portugal: Do No Harm - 1700
  • Bay of Biscay: A Sweet Journey - 1600
  • Bay of Biscay: Sweet Broth - 1500
• Cargo Size 30:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: The Catalans - 3800
  • South Africa: Door to Europe - 2400
• Cargo Size 35:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: The Catalans - 3800
  • South Africa: Door to Europe - 2400
• Cargo Size 40:
  • South Africa: New Economic Hub - 5200
  • South Africa: Table Bay's Luck - 5000
  • Mediterranean Sea: The Catalans - 3800
• Cargo Size 50:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: A New Medicine - 5200
  • South Africa: Table Bay's Luck - 5000
• Cargo Size 60:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: A New Medicine - 5200
  • South Africa: Table Bay's Luck - 5000
• Cargo Size 70:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: A New Medicine - 5200
  • South Africa: Table Bay's Luck - 5000
• Cargo Size 80:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: Great Reputation III - 5200
  • Mediterranean Sea: A New Medicine - 5200
• Cargo Size 90:
  • South Africa: New Economic Hub - 5200
  • Mediterranean Sea: Great Reputation III - 5200
  • Mediterranean Sea: A New Medicine - 5200

If someone finds a good source listing the cities for each mission, I'll add that to the spreadsheet and possibly note the requirements.