Wise in the Hidden
Praising God's wisdom specifically when we see a multitude emphasizes the wonder and importance of the astonishing variety of people. In many places the Sages teach us that we perceive Godliness among mankind specifically through the multitude of human beings. This is hinted at in the story of the Creation: The verse stating that man was created in God's image (B'reshit 9:6) is closely followed by the commandment to be fruitful and multiply (B'reshit 9:7); from this we see that God's image is augmented when there are more people (Yevamot 63b). In another place, the gemara tells us that originally man was created singly so that no person could take pride in his descent; but seems to take for granted that Hashem desired to create many people (Sanhedrin 37a). After all, the prophet informs us that Hashem "created the world for inhabitation", not for desolation. (Yishayahu 45:18.)
A good metaphor is that of light. The Divine light is a pure, white light; yet white light is actually made up of an infinity of different colors which appear white and pure when they are united. (See chapter 60 of my book, Meaning in Mitzvot where this metaphor helps explains the laws of the benediction on the rainbow.) Likewise, the pure light of the Divine is apprehended specifically through the joining together of diverse individuals and opinions.
At the same time, the wording of the blessing draws our attention to the fact even though we gain a special appreciation of the divine through encountering many individuals and being conscious of their varying personalities, we ourselves are not really able to discern and fathom their points of view. This is seemingly reserved only for Hashem, "the wise one of secrets".
Yet in other places we learn that this unique empathy is also shared by a small number of inspired leaders. When Moshe prays for a suitable replacement, he addresses God as "the God of the spirits". Rashi, citing the Midrash, points out the use of the plural, and explains that Moshe wanted a leader who could understand and empathize with the individual point of view of each Jew, just as Moshe could. (Bamidbar 27:16.) In Chasidic thought Moshe is sometimes referred to as a "general spirit" who encompasses the souls of all Israel. (Note that the blessing is only said on a crowd of 600,000 Jews - the number of adult males in the congregation at the time of Moshe's leadership.) An inspired tzaddik or Rebbe is also a general spirit but to a lesser extent; his spirit may encompass many souls, those of his followers, but not all Israel.
Now we can understand the ruling of many Rishonim who state that the blessing "Wise one of secrets" is also made on a Torah scholar of surpassing wisdom (Tur OC 224, based on B'rakhot 58b). Evidently this refers to a Torah leader who is not only steeped in legal wisdom, but also is gifted with the ability to empathize and resonate with others; his followers instinctively feel that he understands them. (This ruling is not cited in the Shulchan Arukh, probably because the Tur himself mentions that we no longer have leaders who attain this remarkable stature.)