This is an incredibly complex question and the answer I'm going to give is not a dissertation or a book, so just keep in mind the fact that I'm glossing a great deal of nuance to get the nugget of an answer.

Let's look at France and Germany individually to compare and contrast. Note that this does not mean that if events in Germany had mirrored those in France, or vice versa, the same result might be expected.

From the initial dissolution of the Carolingian empire in the ninth century, there was an acknowledged king of France. The territory directly controlled by the king was small, and until the mid-13th century was effectively limited to the Île-de-France. This is not to say that he did not wield power elsewhere, but that it was significantly more difficult for him to do so and he was not guaranteed success. In this period the Capetian dynasty (ruling from 987 onward) pursued a policy of aggressive assertion of feudal rights within its domain, assuring it strong and unquestioned authority within royal territories.

In 1209, Pope Innocent III (r.1198-1216) called a crusade against the Cathar or Albigensian heresy, the first use of crusading within christian territory. The Cathars were very popular in the south of France, the Languedoc, and were specifically tacitly supported by the count of Toulouse. The various twists and turn of the Albigensian Crusade do not really concern us except in the end, when the final treaty effectively placed most of the south of France under direct control of the French crown.

This was a massive increase in the power base of the French monarchy, and it came during a period which saw several long-lived French kings, an incredible benefit in terms of maintaining power. Philip Augustus ruled from 1180-1223 (43 years), St. Louis (IX) from 1226-1270 (44 years), Philip III from 1270 to 1285 (15 years), and Philip IV from 1285-1314 (29 years). This chain of long-lived rulers took all advantages given to them. Philip Augustus took the opportunity provided by Richard the Lionheart of England's neglect of his own country and fascination with crusade to savage English holdings on the continent, Louis IX and Philip III consolidated French control in the south, but it is with Philip VI, also known as le Bel, that we can first start talking about France as a proto-state in the modern sense.

Philip le Bel's main legacy in modern history is the destruction of the Knights Templar (thanks, Dan Brown). However, it is less well-remembered that it is Philip that broke power the medieval papacy. This is again a complicated issue that does not really concern us in its details, but after a long back and forth about the ability for the king to tax the clergy, in which the clergy for the first time sided with the king and not the pope (strong control!), Philip had one of his henchmen kidnap and beat Pope Boniface VIII, who died shortly thereafter. Boniface's successor, Clement V, was a Frenchman, the college of Cardinals was quickly made mainly French, and the entire papacy picked up and moved to Avignon in the south of France (though not technically under control of the French crown), where it stayed for 70-odd years. France had arrived as a power strong enough to challenge the papacy at its height and win, and was cohesive enough to survive the 100 Year's War which followed due to the Capetian policy of consolidation of power and exploitation of opportune moments.

The HRE, on the other hand, was set up completely differently. The King of the Germans was elected, although usually from the same set of noble families. They thus could not establish a power base in the same way the French Kings had. Moreover, to become Emperor required a coronation by the Pope, following the example set by Charlemagne (some discussion of that can be found here). This set up what is known as the Investiture Contest, which pitted the German kings and emperors against the Papacy, and caused the papacy to pursue a policy of encouraging a weaker and disunified Empire. In this Contest, it is the Empire which lost, mainly because the papacy was able to incite anti-Emperors, effectively rebel claimants with papal support. This constant back and forth between Empire and papacy went right through the middle ages, prohibiting the emperors from gaining strength while the local lords consolidated their power. Add the disunity caused by the Reformation, and it's frankly surprising that Germany unified into a state as early as it did.

Some reading:

• Tellenbach, Gerd. Church, State, and Christian Society at the Time of the Investiture Contest. Translated by R.F. Bennett. Oxford: B. Blackwell, 1948.

• Kantorowicz, Ernst Hartwig. The King’s Two Bodies: a Study in Mediaeval Political Theology. Princeton Paperbacks. Princeton, N.J: Princeton University Press, 1997.

• Kienzle, Beverly Mayne. Preaching in the Lord’s Vineyard: Cistercians, Heresy, and Crusade in Occitania, 1145-1229. NY: York Medieval Press, 2001.