I was worried about it as well, but for the sake of being able to poke shift, I went ahead with the catch. I tested the catch several times, trying to get at least a perfect HP stat, which I did, but I still ended up with a crappy Reshiram. Oh well. I'll restart the game when the English version comes out.
I was curious if it was possible to determine the number of frames it takes, and through trial and error, once you hit the Reshiram/Zekrom with high HP, that gives you a sign that it should be flawless or near flawless. But again, I'm only shooting in the dark here.