Indonesia does not allow dual citizenship
Indonesian citizenship is given to:
1. A child born of the marriage of an Indonesian couple;
2. A child born of the marriage of an Indonesian man and foreign woman -- the status of which does not cause dual citizenship;
3. A child born of the marriage of a foreign man and Indonesian woman, both of whom request Indonesian citizenship for their child -- the status of which does not cause dual citizenship;
4. A child born to an unmarried Indonesian woman, the status of which does not cause dual citizenship;
5. A child born in Indonesian territory that is not provided with citizenship by his or her parents;
6. A child born in Indonesian territory whose parents are unknown;
7. A child born in Indonesian territory whose parents have no citizenship.
http://www.expat.or.id/info/revisiontocitizenshiplaw.html
It appears that Obama couldn't have legally been registered as an Indonesian citizen unless he was born there. (certainly someone would have noticed that Obama didn't look like his Indonesian "father")