There are certainly many examples of [relatively] weak manual gearboxes out there. The Volkswagen Fox, which were ALL manuals, had notoriously weak transmissions of both 4 and 5 speed variety, but especially the 4 speed. The 091 4 speed in the Vanagons is not the best if worked hard, and the 3-4 slider fork breaking is a VERY common occurrence which is why they make an upgraded part (as well as some other upgrades for the 091). The 091 came out in 1976 and was used in the lighter and mostly less powerful T2 Bus. But by '86, the T3 was equipped with 25 more HP (doesn't sound like a lot, but this reflects a ~20% increase, a pretty substantial amount) and about 600 pounds more curb weight... plus you had an AWD option... adding even more weight.
Many Hondas, especially the higher output Civic Si and Acura Integra, had weak manual gearboxes.
Plenty of Mitsubishi products had some bad ones.
The Mazda unit like my F150 uses (used in many other Fords as well) had some problems that could mostly be solved by switching to proper gear oil (like Mazda uses in their trucks' manuals) instead of the "fuel saving" ATF that Ford specified. Still, these also had a bad problem with the pilot bearing seizing on the input shaft, ruining it and making the transmission need to come completely apart to replace it.
The diesel powered Toyota pickups from the early '80s were all manuals, and they were all awful. '83 + saw an increase in the front input shaft bearing size that helped, you could actually get past 100k miles usually then.
Some of the Renault sourced manuals in Jeeps were pretty bad... again, something that was intended to go behind a modest HP 2.1L Renault turbodiesel, not a revamped gasser inline 6 with nearly twice the displacement.
Still, in many cases, manual gearbox life can and usually is able to be largely extended by how the vehicle is operated. As well as making sure they have a full and clean supply of lubricant. Since manuals will "work" just fine when low on fluid. Automatics won't. An automatic REQUIRES fluid to be present to function. They get low, they act up (slip, flare, etc.) or just quit pulling altogether. Manuals don't. So a small, slow seep of fluid over 100k miles that is gone unchecked means they WILL fail.
The other thing though is the complexity on the control side of an automatic transmission, especially the newer ones. Lots of failures, or at least high cost repairs if not a total failure, are associated with these complex controls. The valve body and all its associated solenoids, sensors, wires, bus bars, lead plates, actuators, etc. is a VERY complicated thing. This means a large liability for *something* to fail. Manuals have none of that. Just some simple linkages to allow your left foot and right arm coordinated by the best "microprocessor" on the planet (the human brain). If that doesn't work, you've got bigger problems than not being able to drive anywhere.
As far as I am concerned, ANY transmission in ANY car that cannot get well beyond 100k miles with no abuse and proper care is a poor unit. Same for an engine, for that matter. And we see plenty of both that struggle to do that.
'