I am an active member of an active virtual airline in the flight sim community. The way we run things might be helpful to creating a successful virtual space agency.
First off, there are two options of creating a virtual space agency.
1-
base it off a real space agency - the benefit of this is you have the missions (some at least, you can create fictitious missions as well) already made and developed for you, and for government agencies, many of the documents are available to the public and can be used for technical aspects of the mission. I fly for the virtual version of British Airways. We fly the same routes at the same times with the same aircraft as our real world counterpart. Another benefit/disadvantage of being based off a real organization is the possibility of support from the real world counterpart. Either the organization will accept the fact that the virtual organization exists and supply them with information to help them run. At British Airways Virtual, we are supported by the real BA and they give us info (company ops and procedures, etc.) that you wouldn't normally get by just visiting their site. On the other hand, the real organization may not approve of having a virtual counterpart based off themselves. They may not like this for a number of reasons and they could sue and your VSA will crash and burn.
2-
create a fictitious VSA With this type, there are no restrictions really at all, but there are some disadvantages. Many people prefer to join VA/VSA's based off of real world organizations due to the fact that they hear about them and want to do what they do because the end user is unable. In turn, option-1 VA/VSA's are more popular, so you went get the booming membership at first. Another set back is that the administration has to create the missions/projects itself. People can get lazy and nothing gets done. The admins have to create engaging-enough missions so that the membership will be inclined enough to fly them.
Another good measure to take in a VSA is to have a pilot client that tracks the end users flights/missions. This makes sure that the pilot is performing the expected mission.
Once a VSA-type has been chosen I will provide more information about that type to help the development process. I am offering my experience in flight sim VA's for helping to develop VSA's. So if you have ideas, just give me a holler and I can provide some input/feedback/constructive criticism.
Anyways, I hope this post proved helpful to at least one person.
Regards, Kevin Burns