It is sort of ridiculous how we find out about power-ups right before, but we had no clue about it up until that point. Kabuto being the non-combat medic-nin he is, it was almost entirely unexpected that he'd have mastered Sage Mode, as well as discovered a realm that Orochimaru himself couldn't enter (not to mention train in). The absurdity of this situation Itachi and Sasuke had inadvertently placed themselves in is what makes Kishi's whole manga seem ridiculous. It makes past powerful characters look worthless and it blurs the known current power levels to unknown degrees. I'm honestly unsure as to who is more powerful Kabuto, Madara or SO6P? It's someone new everyday, practically.
Yet, it doesn't quite ruin the entire set-up, as Kishi is still capable of surprising us with something that will turn the manga around. I doubt he would take it so far, only to ruin it. That's Kubo's job.
