Greetings, Mr. Doody!
The "name"'s Gamecritic83: long time lurker, first time contributor.
Ahh, now THIS is a mental transformation I can sink my teeth into! I love the idea of a meek girl suddenly unleashing her inner badass, and I just so happen to have two Onemanga links to two different mangas that center around that very subject.
1. Othello
http://www.onemanga.com/othello/
A shoujo manga about a girl named Yaya who is constantly taken advantage of by her classmates. One day, when her two supposed "friends" go too far, they end up unleashing a strong, confident alter ego within Yaya. Her name is Nana, bringer of "divine justice" and rock star in the making!
Includes the manga's entire run!
2.Change 1-2-3
http://www.onemanga.com/change_123/
This is the manga that I'm sure most of you guys will enjoy the most, as it also includes some slight physical transformations, not to mention it's a hell of a lot more "ecchi" than Othello. This one is basically the same basic concept as Othello only taken to the next level, and it's been translated by one of my favorite scanlators, SnoopyCool! It's about a shy-but-still-cute nerd girl named Makoto who, due to the absolutely insane three-way special training from her three badass fathers (long story), she subconsciously developed not one, not two, but THREE alternate personalities to help her cope with the mental trauma of it all. Each personality is specialized in a certain art of fighting, not to mention they each take on a radically different (but still slightly similar) physical appearance. Coolest of all, these three alter egos are all too aware of the others' existence and work as a team to take down their foes in a bizarre mental tag-team sort of way. Then there's this highly likeable short guy who discovers Makoto's secret and tries his best to help her, as well. It's too bad only the first two chapters have been translated, so far.
Well, anyway, I hope this satisfies your itch for female empowerment through mental instability, Mr. Doody. 'Til next time everyone!
Gamecritic83