I would say the modern consensus is that he was a pretty extraordinary ruler, but not completely out of the ordinary, and he was just as much a product of his age and circumstances as any other 13th-century personality.

The three major academic biographies of Frederick in English are:

1. Ernst Kantorowicz, Frederick II: 1198-1250. This was originally in German, but was translated into English by E. O. Lorimer (Ungar, 1931). Kantorowicz’s biography was extremely influential, and it’s full of incredibly useful and interesting information, but reading it these days is a pretty bizarre experience. It’s almost a hagiography more than a biography - Frederick was the subject of prophecies, a new Roman Emperor, a saviour, a messiah, maybe a literal god. Is Kantorowicz merely repeating medieval legends or does he really believe that himself? You’re never really sure…here is an excerpt from his conclusion:

“The last emperor of the Romans disappeared from amidst his followers in the radiant glory of the Imperator Invictus, and was spared the knowledge of the tragic fate that overhung his house. His life closed with the “transfiguration” into the Emperor of the End. His imperial career had described no curve, had known neither climax nor decline. From birth his line of life ran arrow-straight to its zenith, then quitted earth and vanished like a comet in the ether: perchance to reappear once more in fiery brilliance at the end of time.” (pg. 685)

For Kantorowicz, Frederick was a sort of idealized mythological Germanic hero, not a man of the Middle Ages, or even of the Renaissance, nor a modern man either, but perhaps a god reborn from the ancient past. Both then and now, Kantorowicz has been criticized for his credulous acceptance of legend as fact, and his almost total lack of footnotes. When you think of Frederick as a larger-than-life legend, it’s most likely because of Kantorowicz.

2. Thomas Curtis Van Cleve, The Emperor Frederick II of Hohenstaufen, Immutator Mundi (Oxford University Press, 1972). When you think of Frederick as something like a modern man transported back in time with his modern sensibilities intact, that’s probably due to Van Cleve. For him, Frederick was far ahead of his time, as if he had travelled there from a more enlightened time. The ultimate conclusion is similar to Kantorowicz (Frederick is unique and out of place/time) but far more rational:

“It is but natural when confronted by the presence of Frederick II in the thirteenth century that one is constrained, by the very singularity of his attributes, to associate him with the Renaissance rather than with the Middle Ages. But it is misleading to insist unduly upon the presence of Renaissance attributes in isolated individuals…He was neither Medieval nor Renaissance — nor was he Modern. He revealed attributes of all these eras, but he belonged to none.” (pg. 531-532)

Van Cleve was still very pro-Frederick, but unlike Kantorowicz, not fanatically pro-Empire and anti-Papacy, and he eventually admits that everyone in Frederick’s story, from Frederick himself to his Papal enemies, was really no more virtuous or evil than anyone else in the 13th century.

3. David Abulafia, Frederick II: A Medieval Emperor (Oxford University Press, 1992). Abulafia sees Frederick as a totally medieval ruler, with medieval mindsets and acting in ways that are completely typical for a medieval person:

“The subtitle of this book [“A Medieval Emperor”] is intended (unlike other subtitles one could cite) to convey a meaning: the medieval emperor and king of Sicily in whom everyone has identified a stupor mundi, a wonder of the world, since the thirteenth century, was in fact a man of his time, and not the displaced Renaissance despot he is generally taken to have been...Part of Frederick's attraction to historians and the wider public has always been that he was supposedly a rationalist, even a free-thinker, ahead of his time, nurtured in the tolerant setting of semi-Muslim Sicily, a friend of Jews and Saracens: the sort of ruler who, to be frank, does not really exist in the Christian Middle Ages, even in Sicily or Spain.” (436-38)

It was the circumstances of his birth that brought him into the defining conflict of the 13th century (he was also the first to rule Sicily and Germany simultaneously, which the Popes did not appreciate), but he was a more stubborn and determined ruler than most, and perhaps more intelligent and competent than others, so he was able to handle this conflict more skillfully than another ruler might have. He also may have been more interested in science and philosophy than most, but he was not alone, and he surrounded himself with people who had similar interests.

So, he certainly was an intelligent and competent ruler. Even other medieval commentators could see that. But at the same time, modern historians would now argue that he was also fully a product of his environment.

Aside from the biographies listed above, also check out Abulafia’s article “Kantorowicz and Frederick II”, in History 62 (1977), pg. 193-210.