Also, they upped the capture rate for the Black/White Dragons so much that they can be caught at yellow health with an ultra ball (after a few attempts and of course a status condition) Save that Master Ball for Kyurem or for Thunderus, though the latter can also be caught easily if you have mean look, hypnosis and some dusk balls.
Save it for Kyurem..... you'll be glad you did (he's a post game legendary dragon/ice and the third dragon)
I usually use my master ball on runners so I caught all the other legendaries with regular balls. If you really don't feel bothered to chase the roaming legendary in this game, use it on them. Otherwise use it on Kyurem as its catch rate is pretty low. And just throwing it out there, that fish pokemon (Basculin?) has a lower catch rate than Reshiram/Zekrom.
Don't use it on Zekrom since it doesn't flee and if you kill him he will still be standind and says TRY TO CATCH ME