Well, I don't think it was an indie game but as it's old and either free or very cheap and someone mentioned it in the other thread I'll recommend Imperialism 2.
It basically encompasses military conquest, diplomacy, industrialization and trade, with the focus on the latter two. But don't worry this doesn't mean some stupid building of things to build more things to build more things - the economy is complex and well designed enough that you'll be constantly struggling to manage all the interlocking elements (cargo fleet, infrastructure, mines, farms, workforce).
Similarily your military and diplomatic strategy will have to be integrated with your eco strategy. If your expecting your workers to demand sugar or strike later you'll have to gain control of sugar - if you do this through military power, diplomacy or trade is up to you. Don't forget to factor in that fjord near your cap when making that decision, though.
Oh, and the AI is very good, it can do naval invasions actually...
The only flaw imo is that the battles are not really the best (and not even playable in MP).
Re: Favorite "Indie" Games
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