I still love Satsuki-sama of course, but she's not the heroine. She's just the most heroic character.
If you think back carefully, Mako has always been the main motivator of change. Ryuko gets fussy, Mako gets her back on her feet. Ryuko gets hopeless, Mako's words encourage her, Ryuko does something stupid, Mako says something really stupid but strangely insightful and the story moves forward.
Mako is basically invulnerable, Mako in a 2-Star is stronger than Ryuko properly synchronized with Senketsu. Even if Ryuko was holding back, there's no way she'd be that much weaker. Mako was totally kicking her ass even when Ryuko was actively defending herself. Mako has split Gamagori's previously-unwavering loyalty, etc.
Mako has pretty much always been the driving force of this series, even if she's usually in the background.