CK,

Those are all valid points and some of the difficulties of Certifying a campus building under EBOM. You need meters for each building and an automation system or someone to record each month's readings. To further complicate matters, many campuses have a central steam and chilled water system, so those would need to be metered also. (Quite possibly natural gas, too).
The problem that I've seen is that although the price of meters has decreased in recent years, the building still needs to be metered and a year's worth of metered data is required for certification. By the time the school purchases, installs, and meters all of the data, the project will take well over a year. It's very tough to get buy in for a project that's well over a year from completion. This is all assuming that the building's efficient enough to meet EAp2 once the data's collected.
Your best bet is to sell the campus on the merits of installing meters to monitor their energy usage. The mere fact that each building is being monitored and the school knows where their energy is going will make them pay closer attention and less wasteful. After the meters are installed, the school can look at energy conservation measures and then begin the push towards EBOM.