What Talisman said. Long story short:
Stock Game = You destroy the fort's cannons, then fight the soldiers in the fort and you get:
> Money + free ship repair
Capture Colonies = You destroy the fort's cannons, then fight the soldiers in the fort AND town and you get a choice:
1. Take the money
2. Give the town to another nation for increased rank with that nation
3. Take the town for yourself and assign your own governor and fort commander
So in the stock game, you could only loot towns, but not actually capture them. Now you can.
Stock Game = You destroy the fort's cannons, then fight the soldiers in the fort and you get:
> Money + free ship repair
Capture Colonies = You destroy the fort's cannons, then fight the soldiers in the fort AND town and you get a choice:
1. Take the money
2. Give the town to another nation for increased rank with that nation
3. Take the town for yourself and assign your own governor and fort commander
So in the stock game, you could only loot towns, but not actually capture them. Now you can.