OK, I know there is a reason for each individual case, but take a step back and ask why is it that Germany took foever to unify? Most of the reasons could equally be applied to most countries which unified much earlier... why did Germany take so long?
Part of it has to do with that nasty Interregnum that the Holy Roman Empire got hit with after the Hohenstaufens were defeated in the 13th century. The HRE's main political leadership was essentially vacant for over a hundred years, so by the time the Habsburgs reached the imperium they were already behind England and France in terms of centralization. The Golden Bull, which was a key part of the Interregnum, has a lot to do with that: the Emperor ceded a lot of his power to the Electors, which increased particularist tendencies. But even with that in mind, the HRE came reasonably close to a modicum of centralization in the 17th century (yes, despite the Protestantism and the Peace of Augsburg that basically carved the Empire in half). Had the Edict of Restitution been fully implemented and not interrupted by the invasion of the Swedish under Gustav II Adolf, the Habsburgs had a pretty good shot at reaching a centralized HRE (well, as centralized as was possible in the 17th century, and far more so than the Empire ended up being). But the later half of the Thirty Years' War screwed that up; with the Treaties of Westphalia, it became impossible for the position of Emperor to do much more than act as a figurehead and rallying point, along with of course a good deal of prestige. Westphalia, by recognizing the theoretical sovereignty of all of the
Kleinstaaterei, broke any semblance of feudal supremacy that the Emperor had over those he nominally ruled.
England, on the other hand, successfully managed to begin reforms along these lines during the Tudor dynasty, and came out of the crucible of the political unrest of the 17th century with a far stronger central political institution than it had had before. And France, unlike the HRE, was able to fight off the foreign interventions (both by Spain during the later Wars of Religion, as well as in the Thirty Years' War and the nearly coincident Franco-Spanish War) and deal with religious unrest with a much greater amount of success than could the Habsburg Emperors.
The long and short of it is, I guess, that there was no real Imperial version of the 'new monarchies' like Spain, France, England, and Muscovy, and what attempts to centralize that they had were too little too late and interrupted by the Empire's enemies and by the religious unrest that was such a huge feature of the sixteenth and seventeenth centuries. So they, like the Italians, had to wait until the advent of nationalism (which, in part, was due to the interventions by other powers against the centralization of the HRE - take, for example, the French plundering and destruction in the Palatinate during the War of the Grand Alliance, which aroused what can only be called a sentiment of protonationalistic outrage in the Germanic states) and the creation of other entities like the
Bund of the 19th century.