Side characters who do things? In MY RPG where I get to make choices? Not on my watch. Seriously, its a problem I noticed in a lot of similar works, since there is a player avatar the developers make them overly important to the point where no other strong characters are allowed to exist. Or if they do, they're handed the idiot ball regularly

Honestly Makoto has a lot of character issues and I have to imagine a lot of it comes from the fact that she kinda had half of Hifumi's character grafted onto her when Hifumi was cut as a PThief.

I never saw Makoto as the 'badass biker girl'. That's her idealized self or rebel, which is what a Persona is, but her actual personality was never like that for me.

Makoto is best girl, she is perfect and precious. She has done no wrong and anyone is says otherwise is lying to themselves. But honestly though, I think that they had to dial back Makoto towards that end of the game, as if she had maintain a strong independent character who made decisions throughout the game then she would have clashed with the main idea of the Persona series, which is taking things at your own pace managing your time. Though she never becomes a trope or a stripped down version of her character either, none of the characters do. They maintain their character traits while not just becoming cardboard cutouts that say the same quote over and over (see Chie's obsession with steak in the P4 sequels) . Which is especially good for an RPG that has a lot of interactions between the same characters.