Many years ago we visited the German War Cemetery at Maleme and as we walked round we passed an old man standing by one of the graves. He turned and spoke to us in German so I had to apologise in English for not understanding what he was saying. "Oh, you are English," he said, grasping my hand. "Thank you for coming." I found it quite emotional and I often wondered if the old boy was visiting a friend. The German cemetery is quite different to the Allied cemetery at Souda Bay, with its row upon row of white stones overlooking the water. In Maleme, the grave stones lie flat with the cemetery on a hill with a slight incline facing (if my memory serves me right) north towards the old airfield and parachute drop zone.
I recommend Alan Clark's book "The Fall of Crete," published in the 60s and "The Cretan Runner" by Georgos Psychoundakis, as two first class examples of the many books written about the war in Crete, for a better understanding of what happened and why. And I agree with others that you can't cram in too much in one visit. The Chania area is a long old drive from Elounda, Louise, especially in the summer, so you'd be better off making it a two-day trip with a night away in the middle (if you can find accommodation.) Maud's circular tour suggestion closer to Elounda is a good one as well. Jean mentions the little museum at Askyfou. If it's the one I'm thinking of (in the mountains towards Omalos?) the old man there had an extraordinary collection of guns, munitions, tin helmets etc. He also took a bit of a shine to my wife and refused to let us leave until we'd consumed far too much of his raki.