As someone who has driven public buses (not for TransDev) the old saying goes, "there are a 1001 reasons for running late, there are no excuses for running early".
Meaning it was perfectly acceptable to stop for a coffee and be 5 minutes late, but if you were reported as running more than 90 seconds early one too many times, that was the end of your employment.
I'm surprised to hear that so many smart buses are running early, especially as the 'smart bus' system constantly tracks their adherence to the schedule... On their Smart route console (rectangular one between myki terminal and speedo) it shows +1 minute or -5 minute (position in relation to timetable).
Ventura/Transdev routes have the more priority systems on their route than any other operator (slip lanes, traffic light priority, traffic signal holds etc) and at non peak times, they shouldn't need to be getting 'time up their sleeve' by leaving checkpoints early.
My advice is to start reporting early running buses to transdev on their website, you should start to notice improvements pretty quickly, else contact PTV and tell them that Transdev haven't done anything about it.
As a on-call contractor at Southern Cross (standing around waiting for things to go wrong), I see a lot of private rides being offered to Skybus passengers, which seems to enjoy a pretty high success rate, especially when directed at groups of 3-4.
Reading about another price hike makes me want to use my (paid) spare time at SCS to hand out 'did you know you can....' type flyers in the coach terminal.
Travelling to MEL from Geelong is not much better, $32 to travel in a Toyota Coasta or Mitsubishi Rosa.. For a few dollars more I can rent a Hertz, drive myself, earn points, leave when I want to and get as equally as close to the terminal.