That is one of the problems with the default settings, you can only get so many points for upgrading modules, so many modules, and so many new ship and fortress types, it is a lot harder to get everything you may want and I don't believe there is anything you can do this game about it. I personally prefer enabling alternate champion progress, where you unlock those buildings, modules, and new ship types based on the total knowledge you have gathered. The buildings will all spawn near your home station, which is often more convenient.