Catching a flight is the best way to travel to Indonesia. You can land in its capital and start your vacation immediately. Of course, you can opt for a cruise if you have the time. However, that would a trip in itself and you will have very little time to explore the country unless you fly in.
Flying into Indonesia is a comfortable option. Just make sure that you have taken vaccination for immunization against hepatitis A. This is a must for all travelers. Malaria and Dengue too are two big health problems in the country. The combination of tropical climate and stagnating water is the root cause behind this problem. Take adequate precautions against these two diseases
Indonesia is a tropical country and heat and humidity will be a very big problem for those who are used to moderate temperatures. Make sure you have sufficient quantities of water in your hand at all times. Make sure you prefer bottled water even if it is slightly expensive. While Indonesia has good facilities, you cannot afford to take risk of suffering from water borne disease.
You may feel like wearing very little because of the tropical climate. However, keep in mind that Indonesia has the largest population are Muslims in the world and they are very conservative insofar as female attire is concerned. This does not mean you will have to walk around in highly uncomfortable clothes at all times. You can choose your clothes according to your destination.
A visit to the local marketplace should not cause any trouble even if you are in your most comfortable pair of shorts. However, wearing shorts when you are planning to visit a mosque is not advisable. Offending cultural sensibilities is never a smart thing to do in a foreign country. Keep in mind that minority community of Hindus and Buddhists too tend to be conservative in dressing pattern. Try to avoid very tight dresses when you are in Indonesia and you should be in a position to visit all tourist spots, mosques and temples included, without any difficulty.