About that topic Kirito cheating with other girls and that serving as a excuse for Asuna behavior, this ship already sailed long time ago with fake kirito scene, and the reception by the fans wasn't great because looked a cheap plot device used by Fujino.
That being said, it's clear the cheating Kirito will only occour if the player wants that, remember almost all his cheating scenes are tied to player decision, differently of Asuna's scenes where you going to see no matter what you do your only option in this is sometimes you get a hidden scene depending on your levels.
Fujino is lefting how kirito will behave to the player and that will have consequences, and looking the plot so far they will be probably bad for the character, he's a blank slate in this point cheating or not, of course you have his plot is running in the background for other things that may or may not are affected by the players choices, but actually these choices so far are only if you want to see the extra scene or not, with no real impact to the main story, remains to be seen if Fujino will change these mechanics and if this will affect the ending /endins or not.
The phase 1, 2 and 3 is a good concept according to the character POV, Kirito, Inoda and Asuna chapters so to speak, but i don't think that is what is happening right now, Fujino so far move the story from one plot device to next one to move the main storyline Asuna's downfall foward, is not that complex for instance the last update he said himself the only way to move foward her breakdown as using memory manipulation (time travel) altering the past to arrange the future, which is a huge plot convinence when you do that in a story you are basically reseting the whole thing, because you reach a creative dead end to conclude the story.
The way i see it, Fujino only have 4 points/goals to adress right now, Group sex, Pregnancy, Secondary characters fate and the Kirito's final revelation, the story resolution (ending) will be a byproduct of Asuna's sexual activities, the plot is moved by this since the beggining, like Asuna went from HJ to BJ you have a scenario, then the plot continues from this point just to justify the next sex scene variation , and moving the Asuna's fall plot along
About the secondary characters, people are up in arms about it, but the question is how he's going to do and one answer resides in these characters actions, one example Liz how Inoda fucked her, Rape, why because she is a Sadist so actions and reactions, Sugu if Fujino goes that route she's a stalker spy rapist so she will be discovered/confronted/druged and raped, Sinon is the dominatrix who likes to toy and humiliate, she will be played/dominated/humiliated.
Now the plot behind explain how this happen is up to Fujino, One simple example how easy is to come up with something,
Liz could very well want revenge to whoever make Inoda rape her, that was the excuse Fujino gave to Inoda that someone force him to do it, and if i'm not mistaken she does have genius sister who works i think to Rect, maybe she is in the council which make Sugu a easy target, or Inoda just need to tell her who didit and make Liz go after Sugu because he knows that was Sugu and the real reason why she did, that she want Kirito for herself because he was in the toilet jerking off when she talked abou it.