If I remember Prime Base correctly, the initial plan was to wake up the rest of the Project about 10 years after the attack on Prime. Since the programmers of the wake-up program were a bet rushed (an epidemic tends to have that effect on people) they didn't have time to test all of the code, that's why we have the teams waking up at random intervals.
Always had an issue with Prime Base, THE command base for the Project, being tasked with the mission of testing responses with the survivors...sort of like the Pentagon setting up operations in Afghanistan to test counter- AL Queida operations (have to admit, seeing some of the Potomac Commandos having to risk thier well-polished rears in combat would bring a smile to my face!).
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