Here's an excellent answer from the FAQ.

The long and short of it is that Germany didn't effectively unify during the Holy Roman Empire's existence because it never developed effectively centralized organs of government. The why of that remains a contentious question, and likely an unanswerable one given the length of time and number of random occurrences (namely unsteady succession) that pushed the Holy Roman Empire in the direction of decentralization and, ultimately, effective collapse. Germany is also pretty damn large, and was even larger when Switzerland, the Netherlands, and Austria were still part of "the German lands".