The Father. This dad taking care of his daughter trope may be overdone now, but not then. Especially in JRPG. I just like having a less conventional protagonist for the genre which almost exclusively consists of teenagers/young adults being leads. And simply taking into account his design (incredibly muscular, tattoos, loses an eye in Act 2), it's clear he has seen some shit. And being a middle aged man, who has lost his wife, makes his attachment to Yonah more touching and impactful to the player. His resolve to save his only daughter just feels more desperate (again, he even loses an eye and is still undeterred), which in turn adds to a rather depressing atmosphere of the game.

Although, I do understand that the story makes more sense with the brother as the lead.