They probably have their reasons, but it probably comes down to resources ultimately. They decided they could get the most mileage out of their current choices.
Personally speaking, I don't think it would take much to change Annie into a more healthy. A popular suggestion that I like is to change her R into a skillshot like in LoL's cinematic trailer. You would basically lob tibbers like a corki Q (with probably longer range and such of course.)
I think it would be interesting if Annie's stun decayed if she was out of combat for X seconds, but she could keep it up by like auto attacking or e/w spamming.