An integrated European Research Area (ERA) is a critical component for a more competitive and open European R&D system. However, the impact of EU-specific integration policies aimed at overcoming innovation barriers associated with national borders is not well understood. Here we analyze 2.4 x 10^6 patent applications filed with the European Patent Office (EPO) over the 25-year period 1986-2010 along with a sample of 2.6 x 10^5 records from the ISI Web of Science to quantitatively measure the role of borders in international R&D collaboration and mobility. From these data we construct five different networks for each year analyzed: (i) the patent co-inventor network, (ii) the publication co-author network, (iii) the co-applicant patent network, (iv) the patent citation network, and (v) the patent mobility network. We use methods from network science and econometrics to perform a comparative analysis across time and between EU and non-EU countries to determine the "treatment effect" resulting from EU integration policies. Using non-EU countries as a control set, we provide quantitative evidence that, despite decades of efforts to build a European Research Area, there has been little integration above global trends in patenting and publication. This analysis provides concrete evidence that Europe remains a collection of national innovation systems.