It is said that Nigeria possesses a somewhat distorted concept of a federal government.
In general terms, all tiers of government in a federation should share equal power as stipulated by the constitution. The situation in Nigeria, however, is not so. Particularly since the inception of democracy. The principles of Nigerian constitution do not reflect the concept of federalism.
The current situation, and what would appear to be the main underlying problem, is that Nigeria has a strong centre, albeit weaker peripheral states. It is more accurate to compare the system that ties the outer states with the centre to a military command structure.
This heavy dependence on the centre means that the states are unable to enjoy fiscal sovereignty. As a result of this, the states are weak financially. This gives them no grounds to negotiate any independence from the centre, and due to it's heavy reliance must remain subservient to the whim of the centre.
Until the constituent parts of Nigeria's federation are awarded sufficient power and autonomy, along with principles that adhere to a true federal constitution, Nigeria can not enjoy a strong, united system of federation.
This is a brief summary of the problems of the federal system of government in Nigeria. I hope that helps.