Minfilia: pretty close. Nobody seems to dislike her but the villains, and she's oft lauded as a valuable member of the Scions despite being just a manager. Has close ties with the leaders of the city-states despite being head of a(n admittedly benevolent) paramilitary organization. No glaring character flaws beyond her lack of combat abilities, which nobody seems to care about.
Moenbryda: Ehh... despite seeming composed most of the time, comes across as a bit hotheaded (e.g. attacking Nabiales) and is not as capable a combatant as the Warrior of Light. Otherwise, not too far off; is introduced as a familiar, well-known and beloved figure with the right tools and knowledge to solve our present dilemma. Wouldn't say her death was meant to reinforce her superiority (or how she was too good for this world), but as a product of that hotheadedness (attacking Nabriales... again) leading to her fatal wounding and having her choose to do something useful with her already-spent life (like Louisoix intended to). Either way, is repelled and offed rather easily by an Ascian, so not really a Mary Sue.
G'raha: really just a plot device for the Crystal Tower side-story. Introduced as a trickster and just happens to be extremely relevant to the plot, but ultimately makes a boneheaded move against the wishes of literally everyone present. Not enough character to judge?
Ysayle: performs a
High Heel-Face Turn, but still isn't trusted and is disliked by Estinien through most of 3.0. Has the Echo like the Warrior of Light, but uses it for the opposite of its intended purpose (summoning a Primal and intensifying the Dragonsong War). Doesn't think enough and bases her ideals on a fragment of a memory. Transforms into Shiva in full view of the
Gration, giving the Garleans reason to intensify their invasion of Eorzea, and is then shot down after crippling the super-dreadnought. Characters are sad she dies, but it's because they lost a comrade they came to know during the story, not just because it's Ysayle.
Warrior of Light: pretty hard to argue. Almost universally loved and accepted, has no enemies but the villains, succeeds at most endeavors, and can pick up any combat style in a matter of moons where it would probably take NPCs years of study and/or training. Still, not everybody likes you; if you start out in Gridania some Wood Wailers act like jackasses while you're talking to Mother Miounne, and let's not forget that Teledji Adeledji saw us as an obstacle to be removed from his path. While we are invincible in the narrative, a fair number of job trainers are... less than pleasant until we earn their respect (lookin' at you, Geva), so it's not like we just show up and are treated as the best thing since sliced bread all the time.