The biggest problem within the Spanish military during the commander of the Duke of Alba, was that the powers at the Spanish court were unhappy that they didn't have proper control over the commander of the Army of Flanders and who got promoted. They demanded that every higher officer role came to the Court to get confirmed or at least got confirmation by the Court which took ages.
Under Alba, there was a meritocracy within the army, also called 'the School of Alba'. Soldiers could grow and rise within the army to hold positions, that in other armies would only be reserved for high nobility. The officer roles within the infantry were considered superior to the ones in the cavalry. While it was true that under Alba those officers were related to him or a part of the nobility, they were all highly competent and trained.
After Alba, the Spanish Court gained more control over who got promoted, which most of the time were higher nobility despite not holding the compentency needed for the role.
The infantry officer positions became to be looked down upon as cavalry officers rose to prominence within the army. Further on there was a massive bloat of officer positions in general compared to soldiers.
Especially at the end, the officers often held other roles apart from their role of officer within the Army and were not even close to the army.
If the meritocatic nature of the Spanish army remained like it was under Alba, you'd have many more competent officers in charge and a completely different army culture in place as well