It will all depend on the reason for the delay on the SKG-ATH flight. If it was ATC related, I'm afraid there would be no right to compensation.

Though you may want to check the flight history for the aircraft that executed the SKG-ATH flight. If that flight has picked up the ATC delay much earlier in the day (Rather than on the actual flight you were on), you could argue that the ATC delay has nothing to do with your flight, and the delay was due to Aegean not being flexible enough with their schedule at the hub(s) in order to compensate. That would be very tough to argue for a compensation claim, but may - maybe - be a possibility.