Possibly a contender for a 16th century ruler that might fit your remit, would be the Ottoman, Suleiman the Magnificent - threat to all of Eastern and Central Europe, oversaw the expansion of the Ottoman empire, including sieging Vienna (although unsuccessful). Instigated a cultural golden age for his people and empire.
Frankly none of the European commanders stand out as being anything special in the 16th century, IMO.
However, I'd be wary making Suleiman the baddie, after all Hapsburg Spain, with its conquest of vast swathes of the globe: the Americas and the Philippines, and was the number one Empire on the way up at the time. Brutal - their actions killed millions, they plundered the globe for anything they could lay their hands on, and they had probably the finest professional military land force (look up the Tercio) - at least in Europe. However they didn't really have a 'Napoleon' leading them to victory. Obviously some good generals - Gonzalo Fernández de Córdoba, for example - but the Spanish were just a massive behomoth compared to virtually everyone else. If things had gone differently for Charles V (1500-1558) and he had somehow kept the Spanish and Austrian Hapsburg lines together, with all their territory, yeah could be conceived as a threat to everyone else near them....
....however, less successful at interbreeding their own royal family. Caused lots of problems later on.