Regarding Pakistan, the theory I read was that circa 1980 they were Soviet allies, and the State Department either had a warning or a prohibition against Americans going there. Ergo BHO used an Indonesian passport because it facilitated travel.
I would add that it would require time and money to apply for a US passport, so if he already had an Indonesian passport obtained years earlier in Jakarta, using it might just have been the easier thing to do.
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Obamas continued use of an Indonesian Passport after attaining the age of majority is a rather curious phenomenon, all the more curious because no statement has been made in relation to it by any campaign spokesperson.
As an aside, if he had a US passport, his travels to Pakistan would have been likely historically traceable. The use of the Indonesian one gives complete untraceability.
Very interesting indeed.
I simply do not believe he had a valid LBC at the time from Hawaii.