It has nothing to do with reciprocity. Each country decides citizenship based on its own laws- my son is a Canadian citizen because I am one. Even if the US did not recognize his Canadian citizenship, that would have no effect on whether or not he is a Canadian citizen. I have no idea what Indonesia's laws are regarding citizenship, but their determination as to whether or not Obama is an American citizen is completely irrelevant under American law.
Obama would have had to renounce his citizenship in the US to become a citizen there. Its as simple as that.
Again, I have no idea what the law is in Indonesia, but there is no evidence that Obama ever renounced his American citizenship.
You can't go and renounce your citizenship and then get it back as if it never happened, thats why he became a Naturalized rather than natural Born Citizen.
When was Obama naturalized under American law? Is there evidence that (a) he ever renounced his American citizenship and (b) if so, that he subsequently again became a citizen through the naturalization process.