Well to be honest I wasn’t very fond of episode 3 either, although that’s more because I felt it spent too much time on somewhat unimportant matters, especially considering Yusa’s shocking lack of prominence throughout the series (I really can’t stand how they pretend Takajo & Yusa are part of the main cast and even Pooh gets more development, it sounds ludicrous and a really bad move to me).
But regarding Yu being pushed aside during episode 3, I always thought that was to underline the importance of Nao. Charlotte was always going to be the story of Yu going from a mere “main figure” to a “real hero”, but Nao has that “heroine” status from the very start. So early on in the show, it didn’t shock me he would take a step back, because he can’t really do anything, especially when someone as competent as Nao is leading the operation. But even more than that, it’s simply crucial to show Nao in that heroine role, because that’s what she is and in the end, mostly everything that was shown of her back then has become hugely relevant in later parts of the story, and especially to Yu’s own development, so it was really important to show what she is & can do before those elements come into play a few episodes after that.
And regarding Yu’s behavior at the time, let’s be frank - what was he going to do? He’s been warned about the dangers of using his powers the way he did up until now, he can’t leave Hoshinoumi on his own anyway, what is he gonna do? Not play along? Why? How? To do what instead? He doesn’t have good enough a reason to run off on his own, and he can’t go anywhere regardless - if he locks himself up in his dorm room, he’ll most likely be dragged out in no time anyway because unlike in episode 7, there’s really nothing to “respect”.
So he was obviously going to play along because in the end he doesn’t have a choice, but then at this point he can’t really shine in the situations episode 3 puts him through - the way he was back then, he can only go with the flow and watch Nao do her magic, and it’s obvious he would be on the side because he has no reason to take a more predominant role since he doesn’t even see why he’d be doing this, and I genuinely don’t think he had the ability to do so at the time regardless.
I don’t know, it all seems to fit inside the puzzle to me, and I thought so back then too, although I didn’t like episode 3 overall.