As well has highlighting the usefulness of integrating along functional lines, the experience of European integration highlights some of the gaps in the functionalist approach. First of all functionalism ignores the fact that integration doesn't necessarily guarantee continued economic growth and benefits to individuals. Everybody may benefit from negative integration i.e. breaking down barriers, but when it comes to integration in terms of harmonisation etc. When you get to this stage of integration it can be difficult to keep the momentum going. In the case of the EU this problem was compounded by a world depression and resulted in a stagnation of the Community.
Economic realities can give nation states a reason to resist the integrative process.
The most important deficiency in the functionalist approach is that it underestimates the strength and vitality of national interest. Mitrany acknowledges that nationalism is a divisive force and that is why he advocates integration on areas which benefit states and build from there. However the transfer of loyalties which he envisages has not occurred. National ideologies have a life of their own which can persevere despite the fact that the needs of society may now be fulfilled by the functional agency rather than the state. People still identify with the nation-state rather than relating to the more elusive functional organisation.