I played the most recent version of the game, so I'm basing my comments on that. (V 0.3)
I wouldn't say I'm a giant Tower Defense player, but I did get sucked into Plants V Zombies at one point. The idea of a MG TD game is a good one!
The overall graphical look is solid. The stage background is good, and I love the magical girl illustrations when you are buying them! Really nice. In game, they are ok. Just hair, so not quite as exciting. There was also an odd issue where they would stretch and become oval-shaped as they rotated. The audio worked well overall.
Gameplay wise, I realize this is still in development. There definitely needs to be more variety/elements/mechanics. As it stood, I just fill the screen with the "fire girls" and easily beat the game. I could really see the value in the cheaper magical girl, aside from variety. It was hard to tell what was happening when I upgraded characters too. It's on your list, but this really needs a tutorial in game!
In it's current state, this is a great prototype with a ton of potential! I'd love to see where this goes as you improve it.