Honestly, I'm not really sure outside of the "She's a Miqo" reason. I think that's about it. In terms of story she offers the least amount of development or impact compared to any of the other scions. It really does feel like she's just there to look pretty.
Let's look at Alphinaud. When we were finally acquainted with him, he spent almost every moment at our side and putting himself in the thick of it. He transitioned from a boy with a naive outlook on what could be, into someone who sees things for what they are and makes educated, experienced decisions. He is a well written character that continuously develops alongside Alisae, constantly trying to prove himself.
Urianger is a man that has the best of intentions at heart, but his methods of bringing about those intentions can be brought into question. While I'm an old timer and trying not to spoil things past heavensward, I don't want to accidentally spoil anything for you here. I will say that he is a man who is very much worth keeping an eye on, as his development is some of the most interesting the game has to offer. His tendency is played on and followed up on, and contributes to his development as a character even going into Shadowbringers.
Thancred is my personal favorite of the Scions. He has visible development and charm that you have likely taken notice of going through ARR and Heavensward. Even after the events of the ARR ending quests, he still finds space for some humor amidst his new, edgy persona. I place Thancred far above Y'shtola because he not only contributes to the narrative in his own unique way but also undergoes varying degrees of character development even after the tragedy that he suffered(although i'm not a fan of how he was handled in Shadowbringers).
As you said, Y'shtola is largely absent throughout many of the game's events. She does not contribute as much as the others, yet she is held in high regard by the community. I'm not sure why. Even in Shadowbringers, I failed to see any real form of development in the launch content. She continues to be an enigma, and after having played for as long as I have (from Beta to Present Day) I just don't care much about her at this point. I wouldn't mind being left with the other scions if she just vanished or died. Hell, we have characters being introduced in this new expansion that have blown her out of the water in terms of development and general likability.>! Her absence from the majority of Stormblood doesn't help her case. At this point i'm convinced she mostly exists to continue to cheat death and deliver nothing substantial except sass. !<
If you ask me, Derplander (the name given to the WoL seen in trailers and promotional material) or Thancred should have been the representatives in Dissidia. Hell, maybe even Yda. The absence of both Y'shtola and her development just doesn't make her a good flagship character. She's a cat girl with sass and a goth outfit, and apparently that's good enough for a lot of people. Unfortunately, it's not enough for me and some others. I want to get to know her like I have gotten to know the others, and it just hasn't happened in a very, very long time. If you ask me what I consider to be the proper flagship character (aside from WoL), it's Thancred. He's the most memorable Scion in my humble opinion.
Let the downvotes commence.