COP stands for Conference of the Parties, the Parties being the countries that ratified the United Nations Convention on Climate Change (UNFCCC). 

With the entry into force of the Kyoto Protocol, the already challenging intergovernmental process will have a new layer of complexity dur to the initiation of the COP/MOP process.

If a matter is dealth with under the COP, it will allow non-Kyoto Protocol Parties to block decision-making on an issue that may be related to the Kyoto Protocol. Countries that are not a Party to the Kyoto Protocol (like the USA, who signed, but did not ratify it), will not participate in the deliberation of the COP/MOP. This may impact the relative leverage of the existing coalitions under the COP/MOP as compared to those formed under the COP.

Source: Navigating the COP/MOP, by Eco Ressources and Helios