Getting around in Indonesia (Jakarta)

Hi Jakarta forum,

I was thinking to visit Indonesia in September for about 2 weeks, preferably rather low-key with a backpack, and was wondering what's the best way to get around.
Are buses and trains Ok?
I imagine there is a lot to see, and 2 weeks are quite short, and everybody has their personal preferences, but I'd be grateful for recommendations/tips! I'll probably get in via Jakarta, and was thinking to perhaps not see Bali, unless I'm convinced otherwise.
Thanks in advance!

Martin