I mean, that's the things, both endings were conceived by Fujino way back when Part 1 seemed basically set in stone with how everything would go in this most standard and cliche ways of Fujino works even if he had dragged it for a bit longer than usual. While I'm unsure about Part 2's soft reset (It may always have been planned that way after all), it's VERY clear Fujino never originally intended for at least Suguha's plot to go the way it has, he clearly did a complete 180º change with her in a way he had never approached before with any character in his games. If things were still as they were 'supposed to be' originally back in Part 1, by now Suguha would be heading for a threesome ending with Sinon as both of them being Hebishima's devoted sluts, which would just have been another add-on for Kirito's "suffering" easy to slot in both endings.
Instead, thanks to the back and forth caused by Part 2's rocky beginning, his own life issues, and "getting rid of Hebishima for the sake of the plot" being brought up, now not only have Suguha broken free from him and gone full yandere for her Onii-chan but Sinon is going her own brand of psycho yandere and clearly planning to do something bad to Hebishima, which is something no NTR Man in the Fujinoverse has ever had to deal with, they're supposed to be invincible gods whose dicks trash any girls' personalities and loyalties with no hope of ever coming back XD So it's no wonder they don't exactly fit into the planned endings anymore