I'll admit I've skipped over most of the long replies, but I do still think the original point stands. I've only played the original game (and watched, and tried to forget Advent Children) so I think it helps that I can take what is given in just that game at face value.

It is a weak, weak point in the game. I'm even pretty sure that after they've screwed over Shinra they say "Damn, kinda hoped it worked" "Wonder if we've been wrong all this time" and then just kinda say they need to move on and think of what to do next. So they clearly don't know what they were doing.

If it hadn't been for Shinra, two weapons would still be alive, and the barrier surrounding Sephiroth would still be up, I don't see what the issue is here. Cloud and the others should have just let them duke it out and then do what they feel is best after it was over. If they had been more efficient in stopping Shinra, the barrier surrounding the crater would still be up!

As for the sister ray draining the planets energy, does this even come up in the game? I'm pretty sure it doesn't, aside from the whole "Mako Energy is draining the planet in general" thing. I don't think they really cared about stoping the Sister Ray until it was going to blow up Midgar.