Speaking of wishing well, why is Maya and Ayane able to reset with us?
Is wired one (USER2) actually our ally?
Maya says she's been resetting without Akira for a very long time (in the sense that he's wiped after one or two resets and she always remains). So in her perspective, Akira remaining for so long is the new thing. NAO seems to imply that him getting to know more about his past is also a new thing, and maybe that's why he's been able to remain (but it is also implied that Pareidolia and, perhaps Hiwamari, have been conspiring to make that happen).
We don't know why Ayane remained, that's a new thing from Maya's perspective too. There is the pregnant theory, sacrifice theory, god's chosen theory and roof theory. We just don't know yet.
USER2/Wires doesn't seem to be benevolent as much as he's just calm. His story is that he refused to leave his solitude, and his feet became roots that went out of his room and connected everywhere. Through the wires, he controlled everyone, but didn't ever abuse this power because he would only interfere when strictly necessary to maintain order (because that was written into his code), and so people just stopped believing in him.
He didn't seem to mind, and remained as he was, now much weaker and dying and only able to control the ones that willingly gave themselves to him. Since he seems to only interfere to preserve order, and would not go out of his way to force his will, it could be argued that he's the least intent on fucking with Akira, but he can't help much either.
That somewhat changed during update 0.40, where he seems to have chosen to take a more active role - maybe as a reaction to Pareidolia, that is doing so much to further his own plans.