There are some great walks on this beautiful isle and you could take a stroll by the secluded coastlines, trek the dramatic cliff tops or ramble the rugged countryside.
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I would definitely pick Greece over Malta. No comparison, better beaches, better scenery and better food. I would also suggest simplifying your trip and just visiting Santorini and Crete. Crete is a huge island, there is so much to see and do not inCrete it could keep you busy for month.