What's not included in the Toyota maintenance schedule?

Drain and Fill (not Flush) the transaxle is not in the schedule. My best advice is 30,000 miles, then 90,000 miles then every 90,000 miles after that. Use Toyota's ATF WS

If you are gentle with the brakes (and so use regenerative braking via the Motor/Generators) the brake pads last a long time. How long depends on terrain and the driver, not time or distance.

Brake fluid flushing depends on the humidity of your driving, not time or distance.

Shocks also depend more on road surfaces and driving attitude than any specific time or distance.

Think about replacing the fob battery and the 12 volt battery every 4 years.

 

Brake inspections are in the schedule; look again?

Shocks, bearings, CV joints are a fix them when they fail item I guess.

Transaxle fluid change yeah: not noted, worth doing, the first change sooner, then stretch the subsequent changes. Say 25,000 miles for the first, then 50,000 miles thereafter.

Brake fluid change has been introduced, finally, at least in the 2014 Canadian Warranty and Maintenance Guide (applicable to all Canadian Toyota models, not just Prius) :

 

Coolant around 105k. Otherwise you are good. After all you bought a Toyota, not a Hyundai. There is a reason Toyota will sell you a bumper to bumper 125k warranty.