If Annie's kit is to be given more counterplay, she will need a full-scale rework
Everyone hates Annie and that's cool because she blows people up very quickly and that doesn't feel very nice but the suggestions people keep making to fix her are ... really bad. Primarily, putting a delay on Tibbers or making her Q a skillshot. Offering more counterplay to a champion isn't usually such a big deal because you can just buff them moderately to make up for their newfound lack of reliability and that's fine, but Annie's different.
Annie does basically nothing. Q does damage, W does damage, E makes her tankier, R does damage (both burst and DOT, also does interesting stuff like turret tanking but not the biggest deal ever). Passive makes all of her offensive abilities capable of stunning. You only ever pick Annie for one thing: extremely reliable crowd control with attached burst. Her E is not a reason to pick her, neither are the perks offered by Tibbers being a pet. The problem here is that reliable crowd control with attached burst is... kind of shitty to play against. Everyone's been nuked by Tibbers both in lane and in teamfights and it doesn't feel good.
So you can take away what makes Annie feel bad to play against... but in doing that you've also taken away the only reason to pick her. Making her stun unreliable would be a more extreme version of what was done to Veigar because he actually has other niches (punishing high AP teams, for example), whereas Annie's only strength is what people want to get rid of. Getting rid of that strength isn't a bad idea, but she desperately needs new ones to replace it and ... probably quite a few new strengths given just how strong her stun is.
So rather than propose really small changes that will effectively delete her like putting a delay on Tibbers and making Q a skillshot, can we suggest Riot gives her a proper rework? She really needs one, and I say that as someone who likes Annie quite a bit. If her current kit has counterplay it'll never be good, while if her current kit is good it'll never be fun to play against. Give Annie new things to do other than flashing onto a team and stunning them all, she'll probably be more fun after it to play and face after it.