It depends on what you want to see/do:
If you are interested to visit a large town with lots of monuments, palaces, mosques,... I would recommend Istanbul. The town has very many different faces, you can also go shopping,...
If you want a town for vacancies, for relaxing, swimming, going out, with beautiful landscape, I would recommend Bodrum. The sea there is wonderful, and don´t worry: The town itself is sometimes a bit overcrowded but on the Bodrum peninsula you can still find (almost) lonely beaches, small villages and the pittoresque white cube houses with flowers around them.
If you want to see a traditional town, you can visit Milas. It is not far from Bodrum. Every Tuesday there is a traditional market.