The milk is split. The state structures of the hard won Yugoslav socialist federation are no more. The Balkans are helpless in the face of neoliberalism, and the EU and NATO provide the only way forward for them--at present. At least by cementing the statelets as postmodern nations, NATO membership should prevent Albanian revanchists from launching a war to regain Albanian populations in Macedonia and Kosovo, and should keep Croats and Serbians from lashing out at each other.
Other than that, NATO is really irrelevant, despite its shiny headquarters in Brussels and its 29 members (and still counting). It is the EU that holds the promise of western materialism and freedom to live and work abroad, and that will continue to shape the Balkans, replacing its rich history and culture with a Euro stamp. At this point, Thatcher's TINA (there is no alternative) holds.
The collapse of the Soviet Union expanded the EU dramatically. Ten central European countries joined by 2007, Slovenia the first Balkan state (2004), and Croatia the latest (2013). The EU, as a collection of postmodern nations, has never been a strong voice in international affairs, and was transformed, like NATO, into a looser and hence weaker union of now 28 states, where foreign policy is decided in Washington (OK, Brussels gets to sign off and even mildly dissent). The EU is a more serious organization than NATO, affecting citizens directly, requiring major economic reforms, unlike NATO, which requires almost nothing of new members except open doors for NATO to rearrange and incorporate a few thousand military personnel.
NATO is a paper tiger, more a sign of US prestige and European irrelevance, where member states pay homage to the US as world hegemon, still very much a 'modern' nation. It is the EU that holds the economic cards, and where the future of the Balkans now lies--until the Eurasia project takes off.