Rambam in his Introduction to the Mishnah gives an explanation for the order of every Seder and reasons of inclusion of various masechtot.
For example, Brachot in Zraim:
And he divided the material in the Order of Seeds, as I will say: He began with the Tractate of Blessings (Berakhot). And the reason that required him to begin with it is that when an expert physician wants to preserve the health of a healthy person upon the state that it is in, he begins by ordering the dietary regimen at the beginning of his medical prescriptions. And therefore, this sage saw [fit] to begin with Blessings, as anyone who eats does not have allowance to eat until he recites a blessing. And [so], he saw fit to order Blessings at the beginning of his words, so that he would order the food in a regimen that has substance to it.
Afterward he saw [fit] to organize his words so that it would not be lacking any matter of all the matters, and therefore he spoke about the [entire] category of the blessings that a person is obligated about for nourishment and for the commandments. And the only commandment that a person is obligated about every day is the recital of Shema alone. And it is not correct to speak about the blessings over the recital of Shema before he speaks about the recital of Shema itself. Therefore, he began, "From when do we recite the Shema," and everything that is connected to it.
And afterwards, he went back to the topic of the Order, and that is to speak about the commandments of the seed of the earth. Etc.
Nazir in Nashim:
And after Ketubot is Nedarim (Vows); as the whole section of vows (in the Torah) and its examination is [about] the vows of women, as it is stated (Numbers 30:17), " between a man and his wife, between a father and his daughter." And when the marriage is complete and the woman enters the marriage canopy, her husband has the authority to abrogate her vows. And because of this he made Nedarim adjacent to Ketubot.
And after Nedarim, he arranged Nezirut (Nazirite Separation), because 'nezirut' is also in the category of vows, and when a woman vows to be a nazirite, her husband can abrogate [it]. And therefore, he arranged Nezirut after Nedarim.
and Avot in Nezikin:
And when he finished everything that the judge would need, he started with Avot (Fathers). And he did this for two [reasons]:
The [first] one is to inform that the consensus and the received tradition are true and correct; and that it was received [one generation] from [another]. And therefore, it is fitting to honor a sage of [the tradition] and to place him in an honored status, since the teaching came to him; and he is in his generation like those [sages of the tradition] in their generations. And so did they say (Rosh Hashanah 25a), "If we have come to call the court of Rabban Gamliel into question, etc." They said, "Shimshon in his generation was like Aharon in his generation; Yiftach in his generation was like Shmuel in his generation." And about this matter, there is a great ethical teaching for people: that they not say, "Why should we accept the judgement of x or the ordinance of Judge y?"
And the matter is not like this, as judgement does not belong to Judge y, but rather to the Holy One, blessed be He, who commanded us about it, as it is stated (Deuteronomy 1:17), "for judgment is God’s." Hence it is all one judgement, and they received it one man from another through the passing generations.
And the second matter is that he wanted to remember in this tractate the ethical teaching of each sage among the sages, peace be upon them, so that we learn the virtues from them. And there is no man that needs this thing more than the judges – as when unlearned people would not be masters of virtue, damage would not accrue to the masses, but rather only to [the person in question], but when a judge would not be a master of virtue and modest, he would damage himself and damage [others].
Therefore the start of his words in Tractate Avot was judicial ethics, as he said, "Be deliberate in judgment." And the judge must be restrained by all of the matters that are in Tractate Avot – for example, that he be deliberate in judgement, and not be quick to execute a legal decision, as it is possible that there be a hidden matter in that case, as they said [about such a case], peace be upon them, "A deceitful case." Etc.
