Charge Shot may only have one problem, but that one problem is what kills it, in my opinion: it can't be charged in midair, which forces Samus to charge it on the ground, and, since she can't do anything while doing so, the opponent can easily approach her. If she could charge up Charge Shot in midair, then it would a much better projectile.
Shadow Ball almost totally outclasses it in most ways, especially since it can be charged in midair. Shadow Ball has utility outside of being a projectile, such as recovery, and it's much safer on shield than Charge Shot because of its recoil and shorter ending lag. Furthermore, uncharged Shadow Balls are incredibly useful for stopping enemy approaches and setting up punishes, which can't be said about Charge Shot. Plus, Shadow Ball can destroy opponents' shields on its own, whereas Charge Shot requires a Super Missile follow-up, which is very easy to see coming. And, Confusion allows Mewtwo to re-reflect Shadow Ball back at opponents, so he can throw Shadow Ball out with little fear of having it blow up in his face. Also, are you sure that Charge Shot it more powerful than Shadow Ball? Maybe Charge Shot just has weird knockback scaling, but I could've sworn up and down that Shadow Ball was more powerful.
Aura Sphere is debatable, since its power is dependent on Lucario's damage, but its charging damage can be used to stop enemy roll-ins, it can be charged in midair, and it's slightly safer on shield than Charge Shot because of its shorter ending lag. Overall, Charge Shot is faster and stronger than Aura Sphere, but, once Lucario reaches high-Aura, a feat facilitated somewhat by Lucario's ridiculous recovery on high percentages, Aura Sphere is not only more powerful, but it charges faster than Charge Shot, as well. I wouldn't say that Aura Sphere is more powerful than Charge Shot overall, but I would say that it's more powerful in certain situations. However, you're right about Charge Shot being more reliable.
All things considered, I'd say that Charge Shot's killing weakness is its inability to be charged in midair. I feel like Shadow Ball has more utility, as well as outclassing it in a few areas, and Aura Sphere is debatably better, if only for its charging damage, situational power, and ability to be charged in midair. That's what I think, anyway.