At least, I am not alone 😉
In fact it seems the time needed to crash is random.
By the way, several days ago I did a stress test too and same results : perfect with both pi 2 & 3.
So I think that the hardware of pi is not the cause.
Do you use an official ps3 controler like me (bluetooth)?
Bluetooth is one of my last suspects… if not it remains hdmi configuration or, Retropie itself.
Does someone else has the same issue?
Note that I have recompile the emulators for PI3, with no change unfortunately.