The special system was introduced to create more unique characters in the JAG universe.
It has been shown that people with a unique system are placed in places to allow a quick growth for the people with the system to complete the system's job. In either becoming a runesmith that can create runes to rip space open or to simply Kill every and anything you see. you would be placed in an Ideal location.
People with a unique system have been found to be put in locations close together Especially for kingdom based systems and Production based Systems.
Recently to the system store, they added Special systems to it the cheapest special system only costing a mere 10EP to the most Expensive Costing a Trillion points. There are probably more expensive Systems but I don't know as I can only view up to Tier 60 in the Shop
A researcher's Notes on Special Systems