Was the Holy Roman Empire always very descentralized , or did it become more descentralized with the passage of time? Were Medieval Kingdoms, such as France before the 100 years War, as descentralized as HRE?

Short answer: Both are correct. Yes, the Holy Roman Empire was always very decentralised, and yes, it also became even more decentralised throughout the centuries.

Longer answer: Ever since its conception, the HRE, which was born out of the East Frankish empire, was seen as a kind of federal union of many smaller territories. This fact was generally accepted by the Emperors and all the dukes, etc. There was never a serious attempt to unify the HRE completely in military, economic, judicial, etc. terms. The importance of the dukes continued throughout the middle ages, and the key to being a successful emperor was to get on well with them. You could somehow see the emperor as mediator between the dukes (later the "Kurfürsten", the selected dukes and bishops who elected the kings/emperors), but if the emperor himself was head of a substantially important territory within the HRE, things could get complicated – see below.

Throughout its life, the HRE had to deal with various problems brought on by its legal nature. You may be interested in these five principal problems:

Problem of continuity: Kings/emperors were elected, and even though in practice, dynasties often ruled for long periods of time and the crown very often passed from father to son, elections were always a power struggle and led to many conflicts, the most notable being the German "Thronstreit" ("throne argument") between the Staufers and the Welfs at the end of the 12th century.
Problem of dualism: Many emperors argued that based on various judicial documents, they were in fact the one and only ruler of the HRE, put in reality, they always struggled against all the princes, dukes etc. of the HRE on one hand and against the Pope/the papacy on the other hand.
Problem of organisation: The HRE never managed to establish institutions that ran and organised the HRE as efficiently as France or England (which had become centralised kingdoms early on) did.
Problem of allodialism: Related to the feudalistic structure of land ownership. Most land was owned by the nobility of the HRE, which meant the emperor often had a hard time dealing with questions that required attention to land and its ownership.
Problem of coherence: The internal differences meant it was often almost impossible for the HRE to act as a coherent body, especially in matters of the exterior. The difficulties of communication meant that a sense of belonging was almost exclusively created by the physical presence of the emperor. This lead to some territories becoming traditionally loyal to whoever was emperor (for example Franconia, areas on the middle Rhine and Swabia), others being traditionally opposed to the power of the emperor (territories at the periphery of the HRE – northern Germany, the southwest and other areas on the border), and others that kept switching their allegiance (for instance on the upper and lower Rhine).

Regarding the last point: Only at one point, during the 15th century, the HRE compacted internally due to pressure and danger from the outside. This didn’t last long, however, as then came the rise of Protestantism and the 30 Years’ War, ended by the peace treaty of Westfalia in 1648, which lead to even further fragmentation of the HRE and made the emperors even less powerful.

One of the main factors in the drifting apart of the various parts of the HRE was the rise of Austria as a great power. After the marriages that emperor Maximilian arranged for himself, his children and his grandchildren, the Austrian territories (or, in order to circumvent the controversies surrounding the usage of the term "Austria", let’s call them the Habsburg territories) included places like Hungary and Bohemia which were outside the HRE. This lead to the Habsburgs focussing more and more on their very own territories (the "Hausmacht" – "home rule") and neglecting their duties as emperors of the HRE more and more. All emperors from 1438 onwards were Habsburgs, you can probably see why this is important. The same trend was continued later also by Prussia and other, smaller territories of the HRE.

By the end of its lifespan, the HRE was, as Voltaire aptly put it, merely an "agglomeration" that was "neither holy, nor Roman, nor an empire" (Essai sur l'histoire générale et sur les mœurs et l'esprit des nations, Chapter 70) and when it was dissolved by emperor Francis in 1806, you could say that nobody really cared because the HRE had become so power- and pointless and its emperors, the Habsburgs, were focussing almost entirely on Austria (which had become the Austrian Empire in 1804 – Francis was a double emperor for two years, Francis II of the HRE and Francis I of Austria).

If you’re interested in this topic, I also recommend you look into the history of Italy during the middle ages. The northern part of what is now Italy was party of the HRE, but due to a few factors (the cultural and linguistic divide being one, the geographical difficulties of crossing the Alps to get there being another, etc), the problems and the fragmentation of the HRE were even more pronounced there. This resulted in extreme forms of parochialism, or "campanilismo" (a term coming from the allegiance to the bell tower, or "campanile", of your hometown) in northern Italy and later the emergence of city states such as Florence. It was always a huge task for emperors to go to Italy and attempt to exercise their (albeit limited) powers there. However, bear in mind that going to Italy (Rome in most cases, there were only three exceptions) was required in order to be crowned emperor by the Pope. Some emperors focussed on the "Italian question" more than others, for example, Frederick I (Barbarossa) went to Italy six times (staying at least 3 years in most cases) – he was aggressive on these occasions and also got caught up in struggles between various Italian communes, too.

Regarding France and England, other people probably know more than I do, but I’d say these two countries started off as decentralised areas, too (think of the Heptarchy, or seven Anglo-Saxon kingdoms of England), but not only did they manage to turn into centralised kingdoms – they also did so within a very short period of time.

Hope I managed to answer your question to some extent. Regarding sources and further reading, most of the stuff I know is in German, but I’d gladly recommend some excellent books to you if you speak the language. For English works, your best bet is The New Cambridge Medieval History (David Abulafia/Martin Brett).