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Well this is only my opinion but I have been to Cyprus twice, Protaras and Paphos and I was disappointed with both. I have now crossed Cyprus off my list and do not intend returning unless someone can convince me otherwise.
I used to work in Crete, Rethymnon, and loved it. There is lots to do and the beach stretches for miles.
The best thing is to read the reports on here and the resort reports and see what you think as everyone is different and are looking for different things on holiday. Also it would depend on when you were looking at going. Crete in October could be nice but is not guaranteed as I have know it to rain heavily for weeks, Cyprus in October should still be hot.
Good luck.