I have been to Crete many times before, it is just too big to see it all in one or two visits! My favourite area was Chania. Every time we go we stay in Maleme in the same hotel, we are very pleased with Takis and Maria. Chania doesn't look like an island but like a mainland mostly. You are in the beach now and after half an hour drive you may be lost in mountains. I like the wildness of this area, I think it matches with the wild nature of its residents. The typical Cretan man always has a moustache, speaks loud and heavy (not a word of English and even if he speaks English you will not understand him!) and seats all day in the kafenio (coffee shop) to play cards and do his chaplet. The Cretans can play their chaplets from one morning till the other morning, they can do only that and nothing else!
Chania has nice beaches all over its coasts, but I think the best thing to do is discover the villages in the centre of the prefecture. Rent a car for a couple of days and go from one coast to the other. Sfakia on the southern is very beautiful and picturesque but the road is awful. Be careful when you drive because all roads in Crete are not good.