The development of Hegemony was a long and very iterative process, and a lot did get left on the cutting room floor. If there are any files in particular that you're interested in, let me know and I'd be happy to share what I remember.

Patricius is right, the ruined buildings near cities are what's left of the old villa feature from the original Hegemony. At the time we were trying to model how Philip would promote new generals by giving lands to members of his Companions. When we started Gold we quickly realized this was going to be a problem now that player's could play any faction on the map. Not only did the historical analogy not hold up as well but the majority of villas were concentrated in Macedonia with relatively few spread around the rest of the map. We considered placing more villas around the map for other factions, but after looking closely at the feature we decided that, although it added flavour, it didn't provide any "interesting decisions" (to quote Sid Meier) and was also harder to teach then just awarding the generals directly.

The ruins you noticed along the Danube were placed as landmark and don't do anything on their own. There's an objective later in the game where you need to position a fleet at a couple points along the Danube and those ruins were meant to make it easier to find the right positions.