The vague memories I had of Greece are of stray dogs & a desolate Olympic park. Ein bisschen traurig to say the least. Marls & I totally redeemed my perception of Greece with our amazing August 2016 adventure to Mykonos and Santorini.
Potential itinerary: MUC to JMK, ferry JMK to Naxos, ferry Naxos to Paros, ferry Paros to Santorini, JTR to MUC.
Daily direct flights from MUC to ATH on Lufthansa or Aegean Airlines. Once in ATH, daily & cheap direct flights & ferries to JTR or JMK via Ryanair, Aegean, or Ellinair. Between the islands, a ferry is the best option because all flights are routed through ATH.
Direct flight MUC to JTR (Santorini/Thera) on Lufthansa on Saturdays. Other flights from MUC stop in VIE or ZRH.
Daily direct flights VIE to JTR on airberlin, Austrian Airlines or Niki (Austrian discount airline, part owned by airberlin).
Direct flights almost everyday from ZRH
Flights from SZG always stop in VIE
Cheap & direct flights from MUC to JMK (Mykonos) via Volotea (Spanish discount airline) on Friday & Tuesday.