What questions of the Minoan and Mycenaean civilizations remain unanswered?
One question or mystery remaining for the Mycenaean civilization is whether they had literature or not. It is assumed that only the scribes in charge of the redistributive economy (opposite of our free market buyer/seller economy: supplies were centrally collected then redistributed amongst the population) knew how to write in the Mycenaean script called Linear B, but this has not been confirmed. The absence of any literary fragments or references in extant records suggest that this assumption might be true. Still, the literacy of the Mycenaeans remains in question.
One question or mystery remaining for the Minoan civilization is that of their origin. The Evans theory holds that the Minoans--a name derived from the mythological characters associated with the island--were from North Africa. More recent scholarship based on "mitochondrial DNA from Minoan osseous tissue found in caves at the Cretan Lassithi plateau" (May 14, 2013, Nature Communications, “A European population in Minoan Bronze Age Crete,” by the Greek and American research team) holds that Minoans were "comprised of local Europeans." They assert that Evan's North Africa theory is "refuted" because of genetic and distance analysis. Origin and language (e.g., Linear A) in Minoan civilization remain as unanswered questions.