The advantage of ISO 14064-1 [*] is that it is much shorter than the 116 page GHG Protocol. The disadvantage is that the extra explanation is required because it is so short, and therefore ISO is now working on a guidance document: ISO 14069.
One of the things where ISO is providing guidance on is scope 2 emissions - the CO2 that is related to the electricity that you consume but that was not generated on your site. In the GHG Protocol approach you just take IEA emission factors. ISO proposes something much more complex. The mechanism is not clear yet, but involves something with type of electricity mix and consumption profile [level 1 and level 2]. Then, the reporting company can choose between taking into account all electricity, or only the mix of the most competitive technologies of the electricity market [attributional or consequential approach]. I needed to sit down with a glass of milk after reading this. It does not make carbon footprinting clearer or simpler. It also increases the choices for companies and therefore makes comparisons between footprints more difficult. Over the last 10 years I did not meet many companies that would be willing to go into this sort of detail for estimating their scope 2 emissions. So this whole idea of estimating scope 2 emissions seems like something for the ideabox.[*] Specification with guidance at the organization level for quantification and reporting of greenhouse gas emissions and removals, 2006

