Blather, rinse, repeat

It could be, but if that was the case, then the writers of the story are obligated to point this out to the audience. I do like when some things are left up in the air to be inferred, but I'm not wild about contradictions that come out of nowhere. To me, those are just plot holes and / or sloppy retrofitting. I understand they didn't spend a lot of time on Last Order, what with perfecting the mind-blowing awesomeness that is Advent Children and all--but they could have at least replayed the game so they could knowledgably address this contradiction.

Besides, it was so awesome in the game when Cloud willed his body back to the ground (talk about chi!) and threw Sephiroth. I as waiting to see that.

As far as Cloud's eyes go, I had always figured that all SOLDIERS down to the lowliest were exposed to Mako. I had also just assumed that most Shinra personnel who might be involved in any kind of battle were exposed to it, too. So that didn't bug me out too much.