I have no problem with changing how you play; one of my biggest problems with solo q is that people don't understand how to counterplay against some champions like Katarina. Instead of staying close to your minions against her, you should probably stay away from them because of her bouncing blade. I'm fine with countering champs with how you play. However, if you're close or far, Annie can ruin your day pretty easily. If you stand inside your minions, she'll hit you with incinerate. If you stand back, as soon as you get into range, she can single-target stun you with disintegrate. If you try to trade, she's got her shield, or she can use her shield to get your stun up.
Most champions people play mid are in the danger zone if they want to poke, or if Annie is close to the wave and you want to CS. My problem is with how versatile her stun is. How many other champions have 3 stuns built into their kit? The only other one I can think of is Kennen, and his is totally different. Yeah, I think that's the biggest issue I have: all of her abilities can be stun if you want them to be. With other champions there's a clear way to avoid their stun that would leave you open, because it's only one move, but with Annie, any spell is a death sentence.