The thorniest question seems, to me, to be how to integrate local government on the city or county scale. Citizenship is fairly straightforward - make the inhabitants citizens of both countries, and let them renounce one and live in the other if they wish. How to ensure that a village has the zoning regulations they want when it was handled by a county in another country seems trickier.
The Netherlands do not allow dual citizenship, so simply allowing all the Belgians/Dutch to chose during an Enclave/Exclave swap wouldn't be possible.
It wouldn't be necessary really, as citizenship is more dependent on your parents. Both of them being EU member states also makes residence somewhat irrelevant too, except maybe with taxes.
