She'd need more queens? It made sense, since one queen was for this simple hive, so an empire that spanned across the entirety of Equestria, and probably beyond, well it'd likely crumble with only one ruler... two technically with you, but still. She'd need other queens the way your world needed governors, mayors, etc. Maybe it wasn't impossible for Ap and Chrysalis to coexist... although, then you remembered that in order  for that to happen, Sunbutt and Moonpie would have to go under... yeah, that still wasn't an option.