The nations concept is a pretty good idea as far as civ-servers go, it's the closest implementation of RTS-genre buildings I've seen and it works pretty well. Ideally I'd rather have it tied to citadel groups, but I can't be too nitpicky it works well as is.

There are two buildings I think that could use some extra features, first:

The Granary

Currently the way the Granary works is by replacing all drops of crops in its' radius, so for things like wheat sometimes it will drop more than 1 wheat when harvested ... however, it will always only drop one seed if manually harvested. This is a problem because it prevents the expansion of wheatfields outside of harvesting grass.

I'm proposing that the Granary tie into the fortune enchantment, so that if you right click a crop with a tool with that enchantment, you get extra seeds/crops.

The other add-ons for the Granary I think should be sugarcane/beetroot support, and adding xp as a potential extra drop from crops.

The Pier

It does what it's supposed to do I guess (I have only noticed an uptick in fish caught, not treasure obtained), this building should be affected by the Luck of the Sea enchantment as the current plugin doesn't give the enchantment a use.