Big problem with her Identity. Her engage with Flash Tibbers is all she's used for. You can't really nerf that without completely gutting her Identity. (of coarse it's her identity that everyone hates.) Also the Stun on her passive is her only CC in her entire kit. Nerfing that would be as problematic for a mage's kit. If this wasn't the case, Veigar would not be in as a terrible position as he is now. Yet in Annie's case, it's more balanceable cause it's her ultimate ability.
In all honesty, I don't actually think her Flash engage is that big of a problem. Cause if it was, We would have just as much problem with
Flash Crescendo,
Flash Curse of the sad mummy,
flash Idol of Duran, or any number of champs that have High, lock down ultimates. Yet we only attack annie, and not just anyone with high lock down, so lock down isn't the defining metric. So how does Annie differ? Gallio and Amumu, arguably have a harder time cause theirs are more close burst and their melee, But the fact that they usually build tanky makes this some what moot. And the different between Annie and Sona is that Sona is basically confined to the support role.
So I would deduced that the only reason why her Stun is problematic is that it's paired with high Damage and High scaling. Is that really a good reason to butcher the only thing going for her in her kit. I'd think it would be more appropriate to just nerf the damage of the ultimate, if the ultimate is too powerful by itself. (well, itself + the stun)
And really? is her Stun problematic anywhere except her ult? Probably not, so it would not really be appropriate to nerf her stun stacking. also Considering the fact that once you have stacked your stun, you are pacified until your ready to cast your ult. Cause if you have to cast your Q or W in defense. You lose it, and would have to stack it up again.
Lastly, Annie is still a staple pick in the LCS as a support. They seem to think that it's actually balanced and won't nerf that. The only way to nerf Annie without nerfing her Support abilities is to attack her AP ratios.