As I understood it, they each used their strongest Genjutsu because, as you say, it was mortal peril. Perhaps that scale of genjutsu was needed to defeat Kabuto's Genjutsu. Kabuto's technique may have been enhanced by Sage Mode.
Originally Posted by Ahmad Jamal
Anyway, Edo Itachi has far, far more chakra than Itachi's ever shown in life. He was weakened when he fought Sasuke, and may have been overstating his fatigue against Kakashi/Guy for the sake of avoiding conflict, but he's still using way more techniques. Consider this to be in line with every character these days... Kakashi has been shown fighting multiple Jinchuuriki, even after his all-day Rampage. Sasuke seems to double his chakra capacity every time he fights; look at him against Itachi, and then against Danzou. Kishi sortof bends the rules, especially when stamina is involved, for the sake of making his fights get progressively more exciting.
To be fair, I think it does Kabuto an injustice. Kabuto's biggest advantage over the Uchiha bros is his Sage Mode chakra capacity. If they were as easily-drained as usual, he'd have already won. But apparently sitting in Susano'o for 5 chapters while spamming Amaterasu and Tsukuyomi is easy for Sasuke/Itachi. I'd expect it to be a natural part of Sasuke's EMS power-up, but in Itachi's case this is simply unfair.
That said, we rarely see any Edos run out of chakra.