For the armada to not be built so large you need to have less piracy in the atlantic so the Spanish state doesn't have the incentive to waste resources on the inefficient convoy system.
Without the convoy system/establishment of the armada and preferably a Netherlands that remains a part of Spain(Perhaps Philip isn't such a bigot as otl) and I can see a Spain that doesn't go bankrupt so soon, have a lot more funds and resources for its wars in Europe and stable economically. Plus you could than see more development of the latin American countries since more capital will be available for the crown to build up pumps and machines for ramping up production of silver from the mine sin Mexico and Potosi in Peru. Perhaps one can also see a development of the Argentian region so that the transportation of silver becomes much easier since shipping it by sea from Buenos aires to Seville is much cheaper than the route whereby ships stop near Panama and go through the carrabian. Finally with access to the Netherlands, Spain will have a solid manufacturing and mercantile/commercial sector and I could see the Hapsburgs retaining their status as the premier power of Europe.