The main reason that Western Europe was concentrated into four Kingdoms (six if you include Scotland and Ireland) while Germany was a mess of principalities, duchies, and such has more to do with both military and political history.

France and Spain were United under their respective crowns due to unification of the nobility for the purpose of reconquest. The French were heavily engaged in fighting the English and retaking French lands that passed to the English due to marriage while the Spanish were fighting and retaking lands from Al-Andalus (Muslims, it was a series of Holy wars that lasted for hundreds of years).

"Germany" was United by a loose confederation under the Holy Roman Empire, effectively controlled by the House of Habsburg. Out of interest of control, it was to the benefit of the Habsburgs that thr HRE was not unified. Thus a series of small duchies, couties, principalities, and such existed under an "elective empire" that was basically always Habsburg controlled.

One fact to keep in mind is that calling Spain united in "the Middle Ages" ignores the fact that Spain did not unite until the very end of the Middle Ages.

In addition, the UK was not united until 1707, although England and Scotland had been in personal union for a century before.

Was the region we now call Germany really a mess because it was populated by a plurality of smaller countries instead of a single larger one?

I've answered this question before in a different form, but I alas cannot find it so I'll repeat it here in brief.

To answer your question, you really have to compare the HRE and France. These are great foils with each other in terms of answering this question. Meanwhile, Spain and the UK are also similar, in different ways.

First, let's go to France and the HRE, circa 1150. Both were basically descendent states of the Frankish Empire, and both suffered from very similar structural weaknesses that were the result of their origin as Germanic successor states to the Roman Empire. What this means in practice is that both, while having centralized leadership, also had a series of very strong local leaders, some often rivaling the power of the King/Emperor. As the medieval period wore on, these two states saw drastically differing histories unfold. For France, the turning point was the hundred years war. While this is often portrayed as England Versus France, it is probably more accurate to describe it as the King of France versus the theoretical subjects of that King. As the war went on, the Kingdom experienced a shift of the King slowly but surely exercising his control over the larger local leaders. The result for France was that, by the end of the war, control had begun the process of deep centralization that was to mark the history of France pretty much to the pressent day. It was by no means complete, but the Hundred Years War allowed the French Kings to bring the local lords to heel and establish that it was Paris (and then Versailles) where control over the entire state was exerted.

Compare this to the HRE. Unlike France, the central authority's attempts to impose more centralized control utterly failed. Part of this was complicated by the reformation and the fallout from that, but in general, those local leaders' power grew rather than shrunk, and attempts by the Holy Roman Emperors to impose more centralized control were almost always brushed off.

In this regard, we can say that the states of France and the HRE were fairly similar in a lot of ways in the 11th and 12 centuries, but within a few hundred years their diverging histories vis a vis the relationship between the centre and periphery would lead the former to become a centralized and modern nation state, while the later was doomed to be a collection of principalities with little unifying authority on the part of the Emperor.

As for the other part. Spain and the UK actually have very similar histories. In the 8th century, Iberia was invaded by the Caliphate, and most was quickly conquered other than a rump state that existed in the extreme North of the penisula. Over the following centuries this rump state expanded, split up, joined up, and expanded some more, until there were the three main states: Portugal, Castile, and Aragon. Castile was actually really a combination of three important principalities: Leon, Galacia, and Castile proper. These were amalgamated under one ruling dynasty, and eventually that dynasty spread to Aragon, which became part of Castile in all but name (officially didn't become 'Spain' until the 16th century). So what we have here is an invaded country of similar peoples, split up into smaller principalities, and slowly amalgamated through conquest and marriage into a larger one. Portugal at one point WAS close to becoming part of this, but local nobility pushed back and ended that attempt. If you're familiar with British history, this story will sound familiar. Just replace 'Caliphate' with 'Norse' and you can see how this might work out. In the case of Britain, all but a couple of principalities were taken over by the Norse, and then the remaining ones pushed back and amalgamated, with the final joining happening thanks to the Stuarts in the 17th century. Spain and the UK also have another thing in common: they are not nation states so much as states of nations. France and Germany, despite both having significant minority populations in the form of Bretons and Occitans, are based around a 'French' ideal. Spain on the other hand has autonomous communities of Galacians, Basques, and Catalonians to name a few, while the United Kingdom has Welsh, Cornish, Scots, and Irish. This is partly a story as to how they were formed; France from an imposition from the centre (and thus, really, a spread of Parisian culture from that centre) and Germany a more modern nationalistic creation of many different German subcultures, while Spain and the United Kingdom are sort of artificial constructs of several different nations whose unity is based as much on dynastic happenstance as it is on any sort of nationalism or natural order.