Commander: Conquest of the Americas is the sequel to East India Company. It uses the same basic engine as the previous game with some upgrades to graphics.
Where it differs from the previous game is, obviously, the setting. You begin with a single fleet of a few ships and a handful of colonists and you must sail to the Americas, find a colony site and settle. Unlike East India Company, where the ports were fixed in historic locations, the colonies in Commander are not. Each game will have different colony sites available and thus ports in different places, with access to different goods.
Once you've founded a colony it begins producing goods, depending on the resources of the site you chose. These might be gold or silver, iron, whales, spices, coffee or many other commodities, all with their own value back home in Europe. You buy the colony's goods (remember this is based on EIC) and sail back to Europe where you sell the goods, hopefully at a large profit. You sail back either with goods produced in Europe to sell to your colonists, or more colonists or soldiers to fill your colony and help it expand. The more colonists, the larger the colony's sphere of influence and thus the more goods it can access, the more goods it produces and the more you can tax from it.
This is the basics of the game. Once your first colony reaches a certain size you can found a second, and so on, giving you more goods to sell in Europe for money.
Also unlike EIC, Europe is not on the game map, and ships are split into two types, coastal and ocean-going. Ocean-going ships can sail to Europe, coastal ships are not robust enough to survive the Atlantic waters and can only sail around the American coast. Coastal ships also have the limited range mechanic from EIC, while ocean-going ships can go anywhere without stopping for supplies. Coastal ships are only useful, therefore, for chasing pirates, attacking the ships of other nations or moving goods or people between your colonies. You might set up one colony as a hub and have your ocean-going ships sail from there to Europe and back, while all other goods are shipped into it by coastal vessels and colonists shipped out.
Additionally to these mechanics, you have four advisors who constantly bother you with missions and advice. You must keep their satisfaction level at an acceptable standard or they have you removed from office. The Royal advisor is a generalist, but mostly interested in prestige and power for your nation, so wants more and bigger colonies, more wealth, and so on. The Economic advisor only cares about your cash flow. The Militar advisor only cares about the number of warships and soldiers you have, while the Archbishop is worried about the wellbeing of your people and international peace. I find this system annoying and the missions intrusive as well as being difficult to achieve on the harder difficulty settings. Especially when the military advisor wants to see five new ocean-going warships come out of your shipyards when you've got no money to pay for them.
Problems with this game are fairly numerous. It's stable and runs fine, but gameplay issues are niggling and largely down to the re-use of EIC engine. For a start, you're not running a trading company here, so your cash flow and bank balance just aren't done right. You shouldn't be buying goods from your colonies and selling them like a trader, they should be shipped home and sold and you given a tax rate on that activity. You can tax the colonies to help offset the running costs of each one, but the colonists get very upset very quickly at taxation.
Another niggle is that, playing as Britain (it should be England in 1500) you still use the East India Company flag, not the English Cross of St. George.
Additionally, you can't explore in-land so you only get the coastal resources, which is annoying since you can see resources on the map that are forever out of reach. Some kind of inland exploration and colonisation mechanism is needed.
No land battles is annoying, as we've moved away from the maritime focus of EIC and we're colonising the Americas. We should have a land battle engine here.
The other countries you compete with are pointless as well. They rarely attack you, and given the removal of Europe from the map it's very easy to hide your shipping in the vast Atlantic and avoid any naval battles. In EIC you got attacked at choke points like the Cape of Good Hope, but in Commander it's all open water. Gone, as well, is the strategic element of taking key ports to deny the enemy resupply sites. Ocean-going ships don't need supplies.
All in all this is a decent game, but for every step forward from East India Company there's a step back, and I think this means that the predecessor was the superior game.