Superman's Not in Kansas Anymore moment is actually more justified than most examples of this trope, both because Clark is actually from Kansas, and because RWBY has always been heavily influenced by the Wizard of Oz series.
It makes sense that Batman and Vixen are the only members of the Justice League to become Faunus in Remnant since they're the only Animal-Themed Superbeing on the team. Batman being a Bat Faunus is obvious and the reason why Vixen is a Fox Faunus is because her superhero name also means female fox.
Given what Kilg%re says about why he went with the Fountain of Youth approach for the Justice League members, it makes perfect sense why Batman is going through I Just Want to Be Special when he normally doesn't express such an attitude; he felt that way as a teen but got over it, only for the de-aging to reawaken it.
It goes further when you realize that it's a good middle ground between the traumatized child that Bruce would have been in the aftermath of his tragic past, and the brooding crusader who, while not exactly mentally healthy, is at least more cemented in why he does what he does. His insecurities about not having powers can be read as him basically wishing he had them as a kid, a means to avoid feeling powerless and helpless and be able to save his dead parents. However, as he grew older and more cynical, he likely pushed aside these feelings and adopted the Batman trait of disliking powers (or at least being wary and careful with them), because they constantly remind him of just how much he does not have the luxury of those powers. How he has to constantly over-prepare and consider his moves in order to compensate for his normal human nature. With that in mind, it's easy to read his complicated reactions to powers as being a form of jealousy and envy.
It's important to remember that Gotham is a city hostile to powers (though for once Gotham comes out more subtle by comparison). He is not entirely immune to the biases that plague his home, there have been entire comic arcs demonstrating as much. Which makes it all the more interesting that he's having this conversation with Weiss (and for further irony, she's only ever known him as a Faunus).
Superman's powers being limited could be less from the changes made to him than just from the fact that the sun he's drawing power from is merely a simulated version. Even if Kilg%re had gotten the wavelength exactly right, it's unlikely he'd be able to generate the tremendous amount of energy that an actual sun gives off.
When Weiss, Blake, Yang, and Wonder Woman arrive to help their team fight the Grimm in the forest, it seems strange that Batman didn't join them at that moment despite arriving together. That's because after Batman discovered Kilg%re is behind their predicament and thinks he's possessing the Flash's body, he decides to stay back from the fight to observe Flash's behavior to confirm his theory. That's why when he confronts Flash, he brings up how Flash is suddenly slower and gets hurt often during the fight despite not being seen participating in the fight.
Part 2
Ruby's reckless attitude makes a fair bit of sense, given that a major part of her character arc in Volume 9 revolved around her constantly repressing her own traits in the name of being a leader and hero, even at the cost of her own mental health and sanity. Even back in Volume 1, she had a bit of a reckless streak in her attempts to impress Weiss during the Initiation. As such, now that she's started to come to terms with the fact that she can Be Yourself, she seems to be letting loose some of her repressed traits.
Kilg%re and his unknown partner managed to create a massive horde of virtual Grimm. Now, they are much weaker than normal Grimm, but that might be an error in the code that could be corrected. So, if they somehow were to bring the virtual Grimm into the real world, Salem would gain a massive increase to her army. If the theories of Kilg%re's partner being Watts are correct, this is not just possible but likely.
Part Two proves this theory true and Watts' Grimm, modified with regeneration and counters to the heroes of the DC Universe, almost conquer it for him.
