That only happened though, because Estinien changed a lot after he found out the truth about the Dragonsong war.
Before the Aymeric thing came out of left field, I was thinking with all the talk of Ishgard not having a king until someone worthy came along, I figured Estinien would learn about stuff over the course of the journey, and by the end of the storyline (3.5 or whatever) he'd somehow decide to rule over Ishgard, having grown to understand more than just the "man vs dragon" bit, including the importance of unifying the people of Ishgard to bring about a better future. Maybe bring in Ysaile somehow to help bridge that gap between the former heretics and the people inside the city walls. A campy solution but I'm a sucker for characters that become better people over the course of the story.
Still trying to decide which I like better between "guy that learns he's had his head up his ass and becomes better for it" (Estinien) and "illegitimate son that's always wanted to do good but until recently lacked the power to do so" (Aymeric).