The Midrash Shmuel on Avos explains the mishna כל מחלוקת לשם שמים סופו להתקיים the question is who wants the arguments to stand? He explains that since the Beis Shamai helped the Beis Hilel to arrive to truth, they are also praise worthy and maybe therefore the Beis Hilel were preceded by the Beis Shamai because of their humility to hear an opposite view before making a decision.
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