Before reading other answers:
This is a bit of a tricky situation. Nissa skipped over Ajani's priority and immediately started resolving Emrakul's trigger.She put the game into a difficult, if not impossible, state to rewind. In this case, Ajani was apparently aware of Emrakul, but did not catch Nissa in time. However, Nissa's actions could have led to Ajani being unable to verify that there actually was an Emrakul in graveyard and the shuffle is legal.
On the other hand, Ajani is partially responsible for controlling the flow of his turn. If he has extra actions to take, or wants to do particular things with priority, he needs to make that explicit. However, given that he implicitly has priority after Glimpse the Unthinkable resolves (with Emrakul's trigger on the stack), this isn't as big a problem.
This is pretty much a GPE - GRV for Nissa, with a warning. Our choices are to rewind, or not. If Nissa's cards are still somewhat separated, or if the players had notes and agreed on the previous contents of the graveyard, I'd be willing to try and separate them from the deck. Otherwise, any rewind is probably too disruptive.
This admittedly is pretty feel-bad for Ajani, and there's a lot of potential for abuse. I'm interested to hear what other judges think…
After reading other answers:
Pretty much agreed on GPE - GRV, warning, no rewind. It's worth remembering that we're not supposed to consider who strategically benefits from a ruling, just to make the right ruling. That said….
It seems like we should have a tool to fix or deal with situations like this. Specifically
- It's an advantage-gaining GRV
- Which is basically impossible to rewind
- and the opponent had no real chance to stop it
In other GRV/FtMGS scenarios, at minimum, both players are partially responsible - one for committing the error, and one for failing to catch it. Either of them could have stopped one player from gaining an unfair advantage. In other GRV only scenarios, a rewind is usually possible - the opponent is rewarded for their vigilance by not giving an opponent an unfair advantage.
In this case, however, Nissa is able to unilaterally take an illegal action, giving herself an advantage, and force it to stick. This feels similar to GRVs where the opponent can't verify the legality of an action, though it's a different situation.