Besides the obvious MOA sizes, the 6 MOA is much better for shooters with astigmatism under daylight.
Bright daylight will wash away the emitter red dot starburst, even if the brightness is dialed up all the way, and leave the user with a round center dot.
The reason is that the emitter starburst doesn't cover up the circle dot when you crank up the brightness, so the round dot appears much more visible than a 3 MOA or smaller dot.
It's easier for the eyes to see and great for most pistol applications.
It kinda make sense, and I haven't seen it explained this way. You can read about it here: https://www.badassoptic.com/3-moa-vs-6-moa-reticle-comparison/