Why does Seder Nashim begin with Yevamos? A person needs to get married before his wife becomes a widow in need of Yibum or Chalitzah!
Various rishonim, most notably the Rambam in his Peirush on Mishnayos, offer different thematically based reasons for the order of masechtos within a Seder of Mishnayos.
However, Rav Reuven Margolios in his small-in-size but high- in-content sefer Yesod Hamishna Va’arichasa, suggests that Masechtos were arranged in order of size. Masechtos with more chapters were placed at the beginning of each order while those with the fewest chapters are at the end. He then deals with all the exceptions that are found throughout Shas. For example, he deals with the fact that the Three Bavas of ten chapters each precede the eleven-chapter Sanhedrin by pointing out that the three Bavas were previously seen as one large Masechta Mezikin, which was followed by the original Sanhedrin which comprised Makkos as well, totaling fourteen chapters.