Nobody plays Brand because everyone is playing assassins, and they shit on Brand. People play Annie against assassins because of her stun + her nukes. See a trend? People take advantage of really strong champs to take out equally strong or even stronger champs.
I'd pick Annie against people like Yasuo, Akali, Talon, Zed, and LB, simply because she shuts down their mobility and can capitalize on their moment of weaknesses without them instagibbing me. She's a safe mid pick simply because of how hard she snowballs and her utility and burst even if she doesn't snowball. Third ranked game I played was against AP mid Gragas (pre-rework) and I picked Annie. I wrecked him.
TLDR: People use her because she's friggin' strong, since a lot of other mages are really weak right now. Fix the problem (energy and manaless assassins), and people will either pick her less often, or they'll be able to tone her down without leaving people without a champ that can consistently do well against assassins.