In the new simcity they have regions where people can place cities, and regions can have one or two great works sites which you can't place cities at, but can work toward collectively to develop a project which benefits the entire region. So they could do something like that, so that not only could you decide to build the spires, but you couldn't build something else of similar power. It could just be a radius around "wonders" or something around which no other wonders can be developed, rather than having a bunch of regions established.
Alternatively you could have it so that you get one spire per continent (e.g. North Ro, Greater Faydark, Dreadlands, Toxxulia Forest, Velious doesn't have one b/c dragons said fuck you). First one built works, the rest absolutely won't.