Also, possibly worth noting... I have looked in the .ini files for start bias information, and found nothing relating to this, however, I have played
a lot of Indonesia, and what I've noticed on Perfect World maps is that they almost always (about 4 out of 5 times) start near the archipelago region. Maybe there is some more complex start bias information hard coded into the game, or maybe it just kind of works out that way once all start biases are taken into consideration, or maybe my crazy is affecting my memory and judgement here... still, I find it's incredibly rare that I can't find a way to take advantage of Indonesia's UA on a balanced map script.
Secondly, It's been mentioned countless times... but civs are balanced for a balanced earth-like map script. Not things like Pangaea and Archipelago, so the answer to (civ) is worthless or OP on those maps is "If that's a problem for you, stop playing those maps".
Thirdly, Indonesia isn't necessarily meant to benefit from all her abilities on a single playthrough. The theme and flavor of the civ comes from trying to leverage the wild-ass and sometimes seemingly mutually exclusive goals and directions they push you towards. It is meant to simulate real Indonesia's struggle and often success in uniting wildly opposing and conflicting religions and culture's. The benefit is, each their UA, UB, and UU are all very strong, each in their own right... when used properly and assuming you've implemented them into your over-all strategy wisely.