Its doable, Phillip II respected their institutions, but his son and grandson did not, and even then it was a lucky chance that the Spanish where at war with the French over Catalonia and the fact that they proclaim themselves vassals of the Pope ... so just one of the factors out and you can keep the Union.
In the Geopolitical outcome, a lot of colonial wars with England and later Britain, with France and with Holland ( after all this one of the main reasons of the split ) ... but about later "problems" is a lot more difficult to speculate.