How do I time an EMMI counter?
Solution 1:
The problem with a catch-all answer is that there are multiple EMMI quicktime events, each with different angles (and differently located fatal stab wounds for Samus if you fail!).
I've managed to trigger an EMMI counter a few times now, and I seem to have most luck by ignoring the flash entirely, and instead attempting to proactively react when the EMMI first starts to move (which precedes the Counter flash by fractions of a second).
I have seen no reason to think there's any randomness beyond which cutscene configuration you wind up with, and beyond that I suspect it's something only improved with practice (and the window is very tight!).