I feel like the story has a huge plot hole that everyone has forgotten about.
So... you know how when you start a new game, everyone thinks you're the same Akira as always?
Not Maya, she knew WE were controlling him and that it wasn't the same person anymore, so what happened to that? Did she forget or did she willingfully ignore that and still decided to fall in love "Akira"
It might've been so long ago that I forgot if there was anything to tackle this but at some point it seems that Maya stopped talking about it completely after she realised this new Akira could survive resets and just decided to cope and live in a lie.
another explanation is that she realised that it was still the same Akira, because he technically behaves, talks and acts like the same person, regardless of who (us) is moving and controlling him. But you can also argue that's not a good explanation because during critical choices, we are still the ones that dictate what to do, just like in the "Tsukasa Wizard magic training" choice in this update. We chose, not Akira, he is still a souless puppet.
Maya thought others were reincarnating into him, but she was wrong.
Maya tends to be wrong a lot. Hence why Noriko is damn near a Saint, but a fucking crazy psycho bitch in Maya's opinion.
We also don't actually control Sensei. If he doesn't want to do something then we can't force him.
Hence why we can't talk to New Maya or do half the things we might want. Even if we do tell him to do something, he'll simply ignore us if he wants, like when it comes to Uta's picture which he keeps whether we delete it or not.
Tsukasa is only optionally safe for now, thanks to us. Not that it matters, considering he still has her number and the story will end up going however Sel wants.
Edit: Just to give an example of what I mean by Maya tending to be wrong:
Sensei not being Sensei, the pregnancy theory, Makoto telling Ami about the loops not being her fault, and apparently psycho Ami are all things she's been wrong about.
It's more or less a character trait for Maya to be wrong: