There are a few options:
- Legendary Bird Trio
I would personally use it on one of the signature Pokemon (Yveltal/Xerneas) because the others you can always come back and rechallenge if you knock them out accidentally. There's a bit more leeway with it, whereas the signature Pokemon aren't worth grinding over just to get them on your team, so you may as well use that MasterBall and catch them straight off.
Another option is saving your MasterBall because it makes great back up if you run out of pokeballs against any of the other legendaries,