If the Universe is indeed a simulation, all those "ghosts" could be glitches, codes spawning the semblance of people again like empty NPCs.
If there are indeed parallel realities, as quantum behavior would make one consider, we may be seeing other people from parallel realities by some sort of overlap in realities, similar to how you can listen to two radio stations at the same time while tuning halfway between those two stations, creating an overlap with both
Any of this shit will need a whole lot of evidence though.
Nintendo is selling their IPs to Microsoft and this is true because:
http://gamrconnect.vgchartz.com/thread.php?id=221391&page=1