I've replaced a handful, but given just how many of these there are on the road, and how few issues I've seen, and how inexpensive they are to replace, and the fact that more and more people who have 2-pedal cars are converting them to 3-pedal versions (almost always using USED gearboxes) I'd place my bet on a good ol' manual in any car any day of the week.
The only manual gearbox I have ever personally had "break" was my 1987 B2000 that lost fifth gear at 346k miles. Drove the rest of the way home in 4th, then to the shop the next day in 4th, where I stuck a used transmission sourced for a whopping $150 in it (of unknown mileage) and motored on. This was a truck that had been used for towing and hauling much of its life, too. I very much doubt the lightweight Jatco slushbox that truck would have had as an option could have lasted as long.
Honda and Subie have had a few weak spots in some of theirs, and the Volkswagen Fox' manuals (there were no automatics) were often short-lived, both the 4 and 5 speeds. None of my Foxes ever had any issues, however.