The Visayas and to a lesser extent Mindanao have substantial populations, and constantly growing tourism especially to the former (including Boracay), but are poorly served by international airlines with the exception of excellent frequencies to and from South Korea.
Years ago Philippine Airlines had an intermediate stop at Mactan Airport, Cebu for one of its MEL/SYD flights - only in the northbound direction IIRC - but that's long been ditched.
Like Indonesia's Jakarta, Metro Manila is a magnet for locals seeking employment but it's far from the case that every Filipino lives in MM or indeed on its island of Luzon.
AFAIK, Qantas has never served Cebu (or Clark airport north of Manila).