Alphinaud doesn't take over her role. The reason Alphinaud is as proactive as he is is because he is free to do so. His leadership of the Scions was really only during 2.0 and considering there was only the WoL, him and an amnesic Cid I hardly call it major management work.

Minfilia isn't a combatant. She may or may not be tough though Livia wouldn't have been trying to beat her to death. I also don't see how the Crystal Braves are at all her fault. She had no authority over them. They were allied but independent of the Scions. They were wholly Alphinaud's project.

He does open up and tell us her suffering which could be seen as annoying. She leans on the WoL because the WoL is everyone's pillar of strength. Its worth noting that its her that the other Scions lean on. She feels that we are the only ones she can open up to since others look to her for strength.

It looks like they are now taking the chance to flesh out the Scions. I suspect we will see development for the other missing Scions if we see them again at least in the same vain as Y'shtola. I am hoping this will be the case for Minfilia too as she has a backstory which has plot threads just asking to be brought back and undoubtedly skills we have never seen her use. As I said before, she never lead anything till she was 18. Her youth was learning from F'lhaminn and evading Garlean Agents targeting her. She is a woman who has been living a false identity for most of her life. There is so much interesting story potential there even possibly tying in her Ala Mhigan heritage. After all her father was a double agent working for the Ala Mhigan Resistance.