I agree that the most powerful implementation would be HunterZ's recommendation. Create an addon that is an alt manager, with an API that other addons can plug into. Other addons can then opdep the Alts addon, and if it isn't present, either not expose that functionality, or use their own built-in functionality.
I think making individual addons do persistence of the data really hobbles it pretty badly. There isn't really a compelling reason to use it in that case; it'd be better to just define a standard API for addons to implement for geteting alts, rather than throwing another lib into the mix. Right now, the list of mods exposing alt data is very small, so a standard API for other mods to implement seems like it'd be easier all around. That said, I think a generalized alt manager would go over extremely well.