The premise of this question collapses time and over looks some context. The French were likely more centralized, that is true, but had no empire to speak of in the time you are alluding to 1500s-1600s. The English had no empire outside of the British Isles until the early seventeen century and most of the colonies it established were quite decentralized for centuries (look at all the problems local institutions in colonial North America caused to imperial government)

As to Spain, two issues stand out. One Habsburg Spain was a dynastic state. That is that many of its possessions were held together solely because they were inherited by the monarch. For example, Charles V controlled the Low Countries because it was his father's patrimony and he inherited the possessions of Castile and Aragon from his maternal grandparents. But even the Iberian kindoms were governed separately because they were separate and distinct juridical, political entities.

You might ask why didn't Ferdinand and Isabella consolidate them, or why didn't Charles? Because the king did not have absolute power, and would likely have faced revolts. Charles did face revolts because he was seen as a foreigner, the comunero revolt. Isabella had come to power after a succession crisis/civil war. Spanish royal power was tenuous and deeply rooted in the notion that the king served as an arbiter over the many factions of society. Kings and queens did not rule absolutely. Politically Iberian monarchs strived to implement 'buen gobierno' that is a government that insured the protection of the rights and priveliages of the governed including serving as an arbiter of justice when and if those rights and priveliages conflicted.

Second, the size and distance of the empire made centralization impossible. Officials overseas had to have autonomy to make decisions in the moment precisely because queries to the king could take a year or more in roundtrip. I would argue that more problems arose when officials chose to delay action until royal review than when they implemented a provisional policy and requested royal confirmation. That said the system purposefully set up overlapping authority so that no one official had complete purview over an issue. This structure insured that someone always informed the king of problems but could also lead to stalemates of power.

Although there were weaknesses in the Habsburg system it worked relatively well for centuries. The rise of the British and French came much later. These new empires had the freedom to try other systems. Change was harder for the Spanish because of intertia and the difficulty of reworking or replacing existing systems. It took a change of dynasty to start that process and even then the Bourbons took over a half century to really start widespread change.

On mobile will edit later to add some reading material.

As /u/historianLA said, this question spans a very long period of time, and has given a good overview of the WHY NOT. In addition to that post, I will give an analysis over a shorter period of time, namely that of Charles V. Some say that while he did the near-impossible -- namely hold his large inheritance together -- he had to make significant compromises due to key challenges.

Part I

Ah yes, Charles V, a man legendary not only for his empire, but also for his appetite. What a timely post as we approach his birthday on 24 February, which I celebrate with my family every year!

Charles V was the one and only monarch who held both the kingship of the crowns of Spain (comprising of Castile, Aragon, and Navarre; their overseas empires and their Mediterranean domains) and the emperorship of the Holy Roman Empire (HRE). Both of these domains had their own sets of complications, challenges, and resistance to the rule of Charles. This led to Charles' inability to retain the entire inheritance for his son Philip II of Spain, and over time this led to divergence in policy between the two sides of the House of Habsburg.

Charles faced internal and external challenges, the combination of which forced compromises that led to long-term divergence. In Spain, he faced the Revolt of the Comuneros, the challenge of how to manage and secure his growing global empire, the threat of Moorish raids in the western Mediterranean. In the HRE, he faced the Lutheran Reformation, the incomplete imperial reform initiated by his grandfather Maximilian I, and the inability to gain support from imperial princes. In Italy, he faced the aggression of France. In the Low Countries, he faced a fractured set of states from whom he needed funding. At the same time, he suffered from PTSD.

As the result, he had to make difficult compromises. In Spain, he elevated Castilian nobility against other states and the well-being of the peasants. In the HRE, he relied on private bankers and military contractors, and leaned further on his brother Ferdinand. He failed in forcing Catholics and Protestants to make compromises for the sake of imperial unity. In Italy, he relied on private contractors. In the Low Countries, he gave out privileges for the sake of loans.

All of the above ended up forcing the fracturing of his empire upon his retirement, as we shall see below. But before we fully begin, let us read parts of his abdication speech to understand his mindset at the end of his reign.

... in the hopes of thereby bringing peace among the Christian peoples and uniting their fighting forces for the defense of the Catholic faith against the Ottomans.

It was partly the German heresy and partly the envoy of rival powers that prevented me from fully achieving the goal of my efforts. With God's help, I have nonetheless never ceased resisting my foes or striving to fulfill my mission. The campaigns I undertook, some to begin wars, some to make peace, took me nine times to Germany, six times to Spain, seven times to Italy, four times to France, twice to England, and twice to Africa in a total of four great journeys, not to mention the less important visits I paid over the years to my individual realms. I have crossed the Mediterranean Sea eight times and sailed the Atlantic Ocean twice, not to speak of the journey I made from Spain to the Netherlands for the very serious reasons about which you know.

As I withdraw, I beg you to be loyal to your princes and to maintain a firm understanding among yourselves. Above all, avoid those new sects that plague our neighboring lands, and when heresy seeps over your boundaries, do not delay in wiping it out, or it will go badly for you. I must for my part confess that I have often misled myself, either from youthful inexperience, from the pride of mature years, or from some other weakness of human nature. I nonetheless declare to you that I never knowingly or willingly acted unjustly or with unjust force, nor did I ever command or empower another to do so. If actions of this kind are nevertheless justly laid to my account, I formally assure you now that I did them unknowingly and against my own intention. I therefore beg those present today, whom I have offended in this respect, together with those who are absent, to forgive me.

The man who is much celebrated even today, saw himself a failure at the end of his reign. He considered himself to have failed in achieving the imperial dream of a strong, united Christian empire, that could bring a crusade to Jerusalem.

The start of Charles V's reign

Some of you will remember that on the 5th of January of this year, exactly forty years had passed since the day when, in this same hall, at the age of fifteen, I received the rule over the Belgian provinces from my paternal grandfather, Emperor Maximilian. Soon thereafter, the death of my maternal grandfather, King Ferdinand the Catholic, brought to me the rule over an inheritance that my mother was too ill to administer. Thus, at the age of seventeen, I sailed over the sea to take possession of the Kingdom of Spain.

it was recognized from the beginning that to have Charles as both King of Spain and Emperor of the HRE may not be practical. His grandfather Maximilian, having failed in his attempt to reform the HRE for easier governance, unexpectedly lost his heir Philip the Handsome, the father of Charles. At some point Maximilian had made up his mind to split the inheritance between Charles and his younger brother Ferdinand: Charles was to be HRE emperor, having been raised in the Burgundian Netherlands, and Ferdinand was to be King of Spain, having been raised in Spain. At the 11th hour, Charles' mentors and tutors, which included the future Pope Adrian VI of Utrecht, convinced Maximilian to change his mind and concentrate the inheritance in the hands of Charles.

The highlight of his early reign in Spain was not a happy one, for he had to face the revolt of the Comuneros in Castile. His Burgundian background and entourage failed to endear themselves to Castile, preferring that either his mentally unstable mother Juana or his brother Ferdinand be their sovereign. This led Charles to arrange the transfer of his brother Ferdinand -- who had grown up in Spain -- out of Spain and into Germany. At the same time, he insisted that Castile pay for bribes to ensure his election to HRE emperorship, causing significant worry among Castilian nobility that their new king would be an absentee king. And that even worse, that this king would make them pay for wars abroad that hurt the interest of Castile. Even in the eve of his departure from Spain, there were still unresolved arguments as Castilian nobles asked for guarantees that Charles would not become an absentee king. Naturally, as soon as he departed for Germany, revolt broke out. The revolt of Comuneros was a very serious threat to Charles' kingship, and lasted years. This is the background as he approached the famous meeting with Martin Luther at the Diet of Worms of 1521: he was a weak emperor with little money, no troops, and no history of winsome ways yet.

The peak of Charles V's reputation

When I was nineteen, upon the emperor's death, I undertook to be a candidate for the Imperial crown, not to increase my possessions but rather to engage myself more vigorously in working for the welfare of Germany and my other provinces, namely the Belgian provinces, and in the hopes of thereby bringing peace among the Christian peoples and uniting their fighting forces for the defense of the Catholic faith against the Ottomans.

Fortunately for Charles, he was soon able to build a credible army in Germany, in time for the Battle of Pavia in 1525. His Spanish-Imperial soldiers, comprising a large contingent of German landsknechts raised by his loyal brother Ferdinand, were able to defeat the army of, and capture the King of France. This was soon followed by the Conquest of Tunis in 1534, strengthening his security in the Mediterranean. In Germany, he was able to defeat the Protestant Schmalkaldic League in 1546, giving hope that he could force a theological compromise for the sake of imperial unity.

All of the above -- an incomplete list of his victories -- were impressive. But at the same time, they expose his weaknesses. Financially, he continued to depend on Spanish revenue, Nederlandish financiers, and private bankers in Italy and Germany. For example, the HRE imperial diet refused his request for funding in support of his wars against Francis I of France, arguing that these were private wars, pushing him into further dependence on funds from Spain, the Netherlands, and private bankers. In Spain, he could rely on the humbling of the nobles and cities who lost the revolt of the Comuneros. But in the Low Countries, he tended to give further privileges in exchange for cash. Administrative and ecclesiastical reforms were postponed, leaving his heir Philip II with an intractable problem that became the Eighty Years' War.