Santorini, Mykonos, Naxos and Crete can be easily combined for Greek island hopping.
Others island combinations could be
a) Paros, Naxos, Ios/Santorini
b) Ios, Amorgos, Santorini
c) Milos, Santorini/Folegandros, Sifnos
d) Mykonos, Santorini, Naxos/Paros
e) Crete, Santorini, Amorgos/Ios
If you go to Paros you can do daytrips around the island or get to Antirparos, Naxos, Small Cyclades, Delos.
If you go to Naxos you can do daytrips to Paros, Small Cyclades, Delos.
If you go to Mykonos you can do daytrips to Delos, Paros, Naxos, Tinos, Small Cyclades.
If you go to Milos you can do daytrips around the island, more than 70 beaches! You can also get to Kimolos island.
If you go to Milos you can do daytrips around the island.
If you go to Santorini you can do daytrips around the island- wine tour/sunset tour or get to Thirassia island. Ios is the closest island to Santorini.
If you go to Crete you could do a tour to Samaria Gorge, or to the Ancient Palace of Knossos. You can also find a Land Rover Safari tour or do the tour to Spinalonga Island with BBQ Lunch :)
Just decide on the islands and you'll have plenty of things to do... You'll discover that 2 weeks are not enough for such beauty ;)