According to Ryan Kim of SFGate's The Tech Chronicles article (IPhone battery concerns prompt speculation), The issues with iPhone 3Gs battery problem appears to be a software side issue.
This is according to Aaron Vronko of Rapid Repair, on of the first to disassemble iPhone 3GS. He said that the problem could be the software that don't work efficiently requiring more power that they need to operate. He adds that the inefficient use of power could be addressed in the iPhone 3.1 OS update.
More details on the full article on the link below.
Link: The Technology Chronicles : IPhone battery concerns pr