Some guy at Reddit has conducted a survey on which theories people believe. I found the results interesting!
For example, more than twice as many people believe that Big Boss is replaced with a doppelganger at some point during the game than believe the “Quiet is Chico” theory. More people still believe that Quiet is related to Sniper Wolf, and the majority of people believe she’s related to The End! Of course that’s just one slice of the Metal Gear community.