Agree, smit0847 - the Metro train/ bus route 901 can be efficient during the weekday peak periods as that is when Skybus suffers most delays, with the latter taking almost an hour from the airport to Southern Cross or reverse.
So what you're really saying is if you had looked up the journey planner on the PTV website, deselected Skybus from the small 'further options' tab at the bottom and caught a train within say three minutes (saving 14 compared with your experience) and then caught a 901 bus outside the station in Pascoe Vale Road (couldn't be more convenient - about a fifty second walk from getting off the train if that) in say three minutes (saving another 12) you would have been at the airport in about 69 minutes.
You could potentially save more time by noting that from Southern Cross after about 1300 hours, the most efficient way can be to get a Werribee or Williamstown line train from platform 14, get off at North Melbourne and board the Craigieburn train there, alighting at Broadmeadows. This is because on weekday afternoons, Craigieburn line trains operate anticlockwise around the City Loop (going from SC to Flinders Street then three intermediate stops to North Melbourne.) Best to travel in the second last carriage from Southern Cross on the Werribee or Williamstown trains as that is where the escalators are, and that will also position you on the Craigieburn line trains close to the station barrier gate and hence exit at Broadmeadows railway station. Knowing where entrances and exits are on rail networks can save valuable minutes and make your journey even more efficient.
My best time from Flinders Street (or Southern Cross) to Melbourne Airport is between 55 minutes and an hour using this public transport. My worst trip on SkyBus took above 50 minutes (though I recall under an hour) so at the time for the latter I 'wasted' $15 in today's dollars. Do I consider SkyBus is worth the extra - no, especially because it then involves a transfer at Southern Cross to other public transport that if using Metro means going up in a lift or escalator then down again to the railway platforms.
I also dislike the way on Skybus that suitcases and backpacks are shoved in by passengers - the staff will not assist - on racks, one of which is close to floor level, the other at about chest height. There can then be a scrum upon arrival as impatient passengers try to retrieve suitcases on the bottom when others are stacked on top.