I spent three weeks in 2015 and it was overall a great experience. I went to Jakarta and Yogyakarta in Java, Ubud in Bali, Labuan Bajo in Flores (as I wanted to visit Komodo National Park), and Manado in North Sulawuesi.
It is incredibly beautiful and culturally rich and I found Indonesian people to be very friendly and open to foreigners. Bali did feel a bit touristy but still authentic and interesting. It's useful to bring a Bahasa Indonesia phrasebook as in some places people do not speak English. I would advice to try and balance natural and cultural sites and to try and visit a few of the islands as they are very different from one another. Flights within the country are relatively cheap.