You wouldn't snap your fingers and get a perfect competition overnight. You'd get a series of better competitions. If I were designing it, I suspect you'd have three tiers - one, the elite level, for the schools with big programs to which serious resources are devoted. The lower tier would be schools who want to play Rugby on a fairly casual basis, and generally have one team in each age group. And most schools would be in the middle tier, which would have to be organised into different conferences (based on geography and history). (You could split the middle tier into two tiers, but most schools in this bracket would be fairly evenly matched.)
Importantly, you'd change it over time, based on the size and scope of the school's program and consistent performance measured across a range of criteria.
The critical thing is to take short-term 1st XV performance out of the equation. That isn't how we should evaluate a school's Rugby program.