The story in XBC2 in general is just something that you could basically compare to that of a Ghibli movie: You've got a world that is slowly dying, humanity on the decline, themes of the hubris of mankind, free will and its destruction of and influence on the environment.
And then, on top of all that. . . we get a protagonist who wouldn't feel out of place in a badly written shonen anime. He reflects not one of these deeper themes, and is nonetheless constantly praised and worshipped by the story. Best example of this is his interactions with Vandham: Rex apparently masters in a couple of minutes a technique that Vandham took decades to learn, and then, after his death, he just makes Rex his successor. A little brat that he knew for what, a couple of days at most? And then there's his bond with Pyra/Mythra, which is constantly talked about as if it's this deep and amazing thing, and how they are just so linked to one another, when honestly? Their relationship is nothing special, and any scene the game dedicates to their romance ends up being obnoxious. And then, later, when he unlocks their true power he just does it by. . . yelling about how he accepts her.
What also doesn't really help is how it just never really feels like the guy goes through any lasting hardship. To recap, he begins the story by already being an orphan - which doesn't really matter that much, since his parents died before he was even old enough to know them. Then, when the party lands in Gormott, Azura "dies" - except it immediately turns out that he's fine, so no worries there. When Vandham dies, it does for a moment seem like he gets a couple of good moments - but then, the next day after that, he's already bounced back to being normal, and Vandham is literally never talked about again. Then, later, when Mythra gets taken by the Torna, he has this five-minute-retirement, where he gives up, but all it takes is one pep talk from everyone and he's already willing to fight again. Then, when Nia confesses her love for him, he just doesn't get it, and, just like Vandham, it's never talked about again, unless you count one possible post-battle dialogue that kinda references it. At the cliffs of Morytha, it seems for a moment like he has to deal with Pyra/Mythra being dead - but nah, like I mentioned above, they're fine. And then, in the ending, after such ginormous deal is made out of how Pyra/Mythra sacrifices herself, how she's definitely gonna be dead now, he can't save her, she has her last words with Malos - she's just fine, comes back, and is even two people now! It's just like. . . every single opportunity that Rex has to go through some character-building/developing hardship, the game just instantly yanks it away and goes "Nah, don't worry, it's fine!".
I'm not saying that Rex is fundamentally flawed in regards to his writing. I have plenty of ideas on how you could change the story to make him more interesting and intriguing, like playing out his "retirement" after Pyra/Mythra gets taken by the Torna some more, and have Nia pull him back from it while the party goes on ahead into the Spirit Cruciple without him. Or having it so that Vandham is his adoptive father, which in turn would not only make better use of Vandham, but also give Rex a better chance to actually develop as a character based on Vandham's death.
And then, in terms of gameplay, he just gets way too much exclusive **** thrown at him. Four story Blades, being the one salvager in the party, getting access to Pneuma, and freely engaging with any Blade later on. The last one really should've been just a feature for the entire party in general, outside of course story Blades.
In short, I just feel like Monolith Soft took every opportunity they had to make Rex as underwhelming of a character as possible, while also using every opportunity to hype him up as the greatest thing ever (which, for the record, is also something that bothered me with Shulk when it started happening in the late game of 1). So, really. . . I suppose the reason why Rex just pisses me off so much is because there was a lot of potential there, and it was all squandered - and yet people act like there's absolutely nothing wrong with him (except for maybe his voice). As it stands, he's just my most hated character in the entire series, which in 2 in particular puts him ahead of even Tora and Dahlia.
Oh, and one short last thing: I don't care much for Pyra, either. I'm not gonna go into detail on that, since I think I already wrote a big enough wall of text here. But what I'll say is, her personality is equally underwhelming to me, and her design is probably the most terrible character design I've ever seen in a Nintendo game. I kinda like Mythra, especially after her role in Torna: The Golden Country as well as her father-daughter dynamic with Addam there, but her design isn't much better than Pyra's. Pneuma's design is almost alright, but doesn't quite stick the landing.