It's not a matter of tougher plastic when it comes to production. A lot of people will think if you use the best materials then thing will last much better and in fact it's not the case when you come to production.
First you have to consider the structure, mechanism that were designed in the first place.
Second and the most important thing is the cost, different materials will use different mold and production method.
Last it will come to assembly.
I think Yamato decided to go with the shoulder design to give room for more poseability and what you trade off is the durability.
To make it better you can have diecast metal shoulder joints, but most people won't like it when you suddenly have a piece of die cast joint over there. If you do paint it, people will start complaining that the paint is cheesy and it chips off which bring out another issue. It's undeniable since it's a joint that you twist and move all the time so the paint will chip.
Having a great design doesnt mean you will have the best product at the end of the day, and yamato realize that to fix the shoulder I can see the difference now the pin is smaller in diameter and the shoulder is easier to twist unlike the first one which is tight.
Last and most important thing is end consumer, you don't toy around with such an articulated masterpiece.