I've come around, and I do think that Annie really is a problem. I don't know what exactly need to be done with her, but her simple kit and high burst damage makes her scary. Along with the possibility of an AOE instant cast stun makes her very hard to deal with.
I actually really hate playing as Annie because I feel she is just so linear to play.
How to play Annie:
Step 1: Stack Passive
Step 2: Nuke enemy team
You have now mastered how to play Annie.
2 things probably need to happen before players stop complaining about Annie.
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Her passive needs to be able to expire. No more holding onto that stun forever.
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Her ult needs to be a missle, a lob skillshot, or have some sort of cast time. Make it easier for people to react as it is one of the most gamechanging Ults in the game if used with Annie's passive and every other big AOE ult has a travel time or cast time to it. Gragas, Sej, Ori, Malphite, Sona, Lux, Leona, and others all have some sort of reaction period in their ults that allow it to be dodged given you had the reaction time and tools to do so. Annie feels bad to play against because players feel like there was nothing they could do when Annie Flash-Tibbers them. If Annie receives a change to her R in such a way described, she could actually receive a buff to its range and would make her less reliant on her Flash.
I feel like she is long overdue for a small scale rework (think Ashe level). And I wouldn't be surprised if this happened in the next year. We'll see though.