One of the main problems with the Kyoto protocol is its non-annex 1 category. The developing countries including the other major greenhouse gases emitters, India and China, are exempt from implementing the protocol. The developing nations have the freedom to increase greenhouse gases if that would help them in their development.
The target and the methods adapted by the protocol are not sufficient to reduce the level of emission. In fact, as per the current observations, there has been a steep increase in the level of emissions as opposed to a 5.2% decrease. For the measure to be effective there is a need for massive cut, quickly.
The protocol has a provision where developed countries can earn credits by funding developing countries with reducing emission. This means, the developed countries do not necessarily have to reduce the emissions themselves to earn the major credits.
One of the problems, not exactly with the protocol, but regarding the protocol would be that the major greenhouse gases producer, the United States has not ratified it.