Feudalism and disunity prevailed in Europe during the Middle Ages. However, by the middle of the fifteenth century, several powerful nation states had emerged in Europe.

The Hundred Years' War (1337–1453) was a key event of the late Middle Ages, and its end led to the rise of powerful kingdoms in both France and England. England and France were politically intertwined, and English kings claimed to be the rightful rulers of France. Several English kings had invaded France to press their claim to the French throne during the long conflict. The English won most of the battles, but the French, led by Joan of Arc, rallied. England was defeated and France emerged as a united nation. Another factor which led to the rise of the French kingdom was the decimation of French nobility during the war. England eventually emerged more united, too; it focused its subsequent energies on developing its naval power. The uncoupling of England and France enabled each to develop strong, discrete central governments.

The year 1453 also marked the fall of Constantinople. An Ottoman army took the last bastion of the Byzantine Empire. After this resounding success, the Ottomans became more united geographically and thus a force to be reckoned with by the West.

Spain also became a united and powerful nation state in the mid-fifteenth century. Castile and Aragon were linked through marriage in 1469. A newly united Spain ejected the last Muslims from the Iberian Peninsula in 1492.

Spain and the Ottoman Empire became dominant in the sixteenth century. England and France surpassed them as the leading nation states in the seventeenth century.

As the Middle Ages came to end in Europe, there were several significant changes that allowed for stronger and more efficient governments to control their domains.

For one thing, many monarchs began consolidating their power. For centuries they had relied on more or less indirect rule through a complex hierarchical feudalistic system. By the High Middle Ages, it was becoming clear that this system had inherent weaknesses. Feudal lords too often quarreled with each other to create an effective system of governance. Sometimes they even came into conflict with the monarch himself. Many monarchs responded by taking more direct control over their kingdom. This was particularly the case in France and England. Political shifts, such as the ratification of common law and the establishment of parliaments shifted power away from nobles and towards the monarchs and commoners alike. These shifts would pave the way for more powerful governments by sidelining the power of the nobility.

Furthermore, the increasingly flourishing economy across Europe led to a new mode of political development. As certain cities became wealthy centers of commerce, they increasingly gained larger measures of self-rule. Sometimes this was granted through royal charters. Other times, cities established themselves as self-sovereign city-states. These developments started to erode regional feudalistic systems and replace them with the powerful local rule of well-funded governments.

This question relates to a theme which runs from the Early Modern Era backwards across the Middle Ages: feudal lords and rulers ultimately had competing interests, with Rulers seeking to centralize power under themselves, while the Lords sought to protect their own traditional rights and privileges. Also note that this conflict could turn violent, and struggles between lords and kings did have the potential to spark a civil war.

There were trends within the High Middle Ages which might be worth discussing as far as this question is concerned. The High Middle Ages saw dramatic population growth, bringing with it revivals in trade as well as the growth of towns. I would suggest these evolutions were ultimately to the advantage of the monarchs, given that increased centralization appears to have been a theme of the Late Middle Ages. To quote one historian:

Feudalism finally waned in the monarchical states in the late fourteenth century with the emergence of stronger state structures, as well as the reimposition of the authority of the Roman Catholic Church in much of Europe. Thus, feudal relationships dissolved as the strength of rulers increased and the independence of nobles declined. [John Merriman, A History of Modern Europe: From the Renaissance to the Present (Third Edition). New York: W. W. Norton, 2010, p. 12]

In addition, consider the impact of the Black Death, which further devastated feudal structures across Europe.

In any case, it was with the Early Modern Era that we observe the rise of bureaucratic absolutist states. Here, we see centralization closely tied with warfare. Gunpowder technology was critical to this, in that it destroyed the traditional role of the nobility in warfare. These technological advancements culminated in the rise of Standing Armies, which enforced but also necessitated the growing power of the state. Standing Armies on a national scale require a high degree of bureaucratization in order to function. Political centralization and military necessity tended to go hand in hand.

The major reason for this was the decline of the feudal system.  As feudal lords lost power, monarchs were able to take greater control of their territories and people.

The decline of feudalism came about for at least two main reasons.  First, there was the increase in trade and in the economic importance of the middle class.  This made cities more important and agricultural manors less important in economic terms.  Second, there were changes in military technology.  The rise of such things as longbows and even gunpowder made knights much less militarily valuable.  Large armies were now much more important than individual knights.  These two trends combined to make feudal lords much less important both militarily and economically.  This allowed monarchs to keep greater control of their territory.