So the Kli Yakar uses that parsha to provide illuminating insights into Bnei Yisrael's first Pesach, the parable of the Four Sons, and what it all means for us and how we can apply these lessons to our own lives.
The Universal Lesson of the Wise Son
Regarding the Wise Son, the Hagadah says the following:
What does the wise son say?
"What are the testimonials, statutes and laws Hashem our God commanded you?"
You should tell him about the laws of Pesach, that one may eat no dessert after eating the Pesach offering.
And you shall tell your son on that day, saying, "Because of this, the Lord did [this] for me when I went out of Egypt." (Shemot 13:8)
If your son asks you tomorrow to come, saying, "What are the testimonies, the statutes, and the ordinances, which the Lord our God has commanded you?" (Devarim 6:20)
You shall say to your son, "We were slaves to Pharaoh in Egypt, and the Lord took us out of Egypt with a strong hand. (Devarim 6:21)
....the Wise [Son] shall learn the order of the acquirement of perfection. And this is the order:
 From the beginning, a person must bring his physical essence into the crucible of affliction [kur ha'oni] to refine and purify it from its "rust."
[This is symbolized by the bitter herb/maror].
 And through this, he will come to submission before his Creator.
[This is symbolized by the matzah, as we'll see below.]
 And through this submission, he will come to a recognition of Hashem's Existence.
[This is symbolized by the Pesach Offering, which is symbolized today by the afikomen.]
For Hashem's bringing Yisrael into the crucible of affliction of Egypt was in order to scour their physical essence to bring them to submission, and from within that state, they ended up coming to the recognition of Hashem's Existence.
And the first two are like laying the groundwork to come to the third idea, which leads to knowledge of His Existence because this is the most desirable and the direct purpose above all others: to bring them to emuna in the Blessed One.
The Pesach Offering is the primary objective and the desired final purpose, elicited by the eating of the matzah and the bitter herb: That is to say, the Pesach Offering signifies emuna in Hashem Yitbarach.
The Kli Yakar explains the tremendous power behind the Pesach Offering:
The Pesach Offering [Zevichat HaPesach, AKA "the Pascal Lamb," AKA "haPesach"] bears witness that Hashem's Testimony is Faithful in that Hashem Yitbarach rules over the astrological system, even over the sign of Aries [the Ram], which is the first-born and leader of all the Zodiac [according to the opinion that Nissan, whose sign is Aries, is actually the first month of the Jewish year] and certainly over the rest of the Zodiac. For the mitzvah of the Pesach offering is as Rashi interprets the verse (Shemot 12:3) "And I shall pass over you [ וּפָסַחְתִּי עֲלֵכֶם ]" as: "I shall be compassionate."
He means to say that now you will go out from the authority of the Zodiac, whose functions are compelled and innate, and doesn't have within them the power to carry out any function that derives from compassion [chemlah], mercy [chaninah], and charitableness [tzedakah]. And you shall enter under the Wings of the Shechinah.....through this, we will go out from under the hand of the astrological system and we will stand before Hashem Elokim to enter into the shade of His Wings.
Just like in the other parts of Parshat Bo, we see once again that our deeds and inner spiritual work influence the stars, and not the other way around. Once we whole-heartedly choose to enter under God's Protection and realize that He rules over all and that there is no force greater than Him, we truly have nothing to fear.
It feels counter-intuitive to most people, but in actuality, submitting to Hashem is the most liberating and powerful thing a person can do.
The Symbolism of Matzah and Chametz
As is well-known, matzah represents humility. The pre-Pesach drive to annihilate, throw out, and nullify all chametz (leavening and leavened products) represents the goal of doing the same to our Yetzer Hara, and especially to any unearned sense of superiority and haughty pride. Chametz makes the otherwise flat dough rise just as haughtiness makes us rise in our own estimation.
....the dough of the matzah is "limited;" it does not rise. Similarly, matzah is a sign of freedom because in the merit of our submission to Hashem, our fathers were redeemed from Egypt, as it is written (Devarim 7:7), "Not because of your being greater than all the nations did Hashem desire you, but because you were the smallest."
Chametz is sentenced to burning because anyone who is haughty is judged by fire as seen in the Yalkut (Tzav 480) regarding the verse: "The Olah [Burnt Offering] that burns...." (VaYikrah 6:2) because the nature of fire is to rise upward. Likewise, one who rises upward [i.e., become haughty or prideful] is judged by it.
Although I did borrow a couple of terms here and there from Rabbi Elihu Levine's translation, this is primarily my own translation and any errors are also mine.
For a wonderful rendering of the Kli Yakar into English on Parshat Bo, including helpful footnotes, please see Rabbi Elihu Levine's translation.