Well the thing is, the gem has to specifically be targeted; it gets shielded by the body otherwise. It's specifically described as being more durable than the human body, and the only way it really shatters is by healing the magical girl whose soul it contains to the point where it wastes a lot of energy. Normally this would be about three good fatal blows, if evidence from the Sayaka Vs Kyoko fight is anything to run off of. I'm not sure if the gem is elementally/psychically resistant, but thus far Soul Gems have only been destroyed through massive physical force being applied, despite elemental/projectile attacks being present in the series.
Also, tanking Psycho Boost... doesn't impress me as much as it should. Yes that's incredibly fast and yeah that's more credit than I'd give a normal human. But I'm not arguing in favor of a single rocket; I'm arguing in favor of, hypothetically, hundreds of rockets, plus bullets. Homura has been shown to carry small firearms and an assault rifle as well.
Finally why doesn't she just... like... steal the Pokeballs during a time freeze? There's probably a feat from Red I'm missing that makes this impossible, just curious.
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How many points did Black Turtle win the guru by? Wow that's a lot, a lot!