The struggle for economic resources might not be as bad as you envision. Countries like Germany have excellent social welfare systems with the capacity of processing refugees as quickly as possible. (OK, "as quickly as possible" isn't very quick, but they'll handle it.) The biggest challenge at the moment is getting these people off welfare and into the job market. Sure, because of cultural and educational differences we're probably not going to see many engineers or neurosurgeons, but the people who collect our garbage and do our cleaning mostly aren't engineers or neurosurgeons either. And language barriers are more fuzzy in the EU than in most other places, we tend to get around them. The jobs won't be fancy, but they'll pay minimum wage and give the refugees a purpose and a sense of self-worth. Also, there's no path to integration as straight and speedy as hanging out with colleagues over breaks.
But you're right, it's not going to be easy. It's going to take pragmatic and inspired leadership within the EU, and we're in very short supply of that. On the other hand, these people and their children will pay the future taxes that fund my pension and socialised medicine, all I need to do is make sure they're safe and land on their feet now.