They don't break down. This is t0yota quality.
Manual would have been easier to fix.
The Auto can take more beating, gives you more torque on the wheels, and is easier to drive, especially with a trailer.
The manual gives you better control over the rpm (typical for auto is 1800 rpm up all steepish hills, as that's the stall speed for the converter); and a slightly better fuel economy.
I think there is more maintenance on the manual (clutch and sync. rings), but any repair on an auto would be more expensive. They will last between 500 k and 1 million km before needed though.
There is the issue of the ATF running through the bottom of the main radiator, so that any damage to the bottom part could lead to coolant into the ATF. This hasn't been a problem on the 100 series, but the 90 series has had a few incidents, sharing generally the same design.
When I got my first 100, I wanted a manual (as my 80 was), but because of difficulties finding one (without waiting 5 mnths for production) I settled on an auto. It came as a gift from above, the auto really suits this heavy vehicle. And that was the older 4-speed --- The newer 5-speed is mucho mucho smooother and faster.