well the idea is in the area of employment to look at EU citizenship rather than which Member State you are from .. you could implement the 6+5 rule applying to non-EU citizens.
from the EU's point of view a player of Sporting that came through the youth program of Austria Wien is the same as one that came through the youth program of Benfica, allthough one is portugese and one is Austrian they're both EU citizens and you can't discriminate amongst EU-citizens ..
and that is my whole problem with the 6+5 rule, it takes away from the fact that the EU is in this process of unification and tearing down barriers to free movement and then FIFA tries to implement an new barrier amongst different Member States.
to me it's the same thing as a player born in London not being allowed to play for Everton because there's already two guys from Ipswich and four from Birmingham playing for Everton. (although i do realize that for some people that might be taking it a step too far, it's just how i see the EU in the areas where it has been given exclusive competences).