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Master Balls are only usefull when you want to soft reset a legendary Pokemon, or you encounter something you really want to catch (like shinies and roaming Pokemon). Everything else is something that can be done with a good strategy and a little bit of patience.
I just wished they would give you more Master Balls, so you can actually SR more legendaries without having to trade other Master Balls from other games...
When the first time i play pokemon games, i usually used it on the legendaries because i thought it was really hard to catch them with the other ball. But now, i catch them with any type of balls that i have in my bag. xD
In Pokemon Colosseum, I used to do the "Master Ball Glitch" on Shadow Pokemon, and it worked pretty well but made the game to easy. Still enjoyed the game though.
I used to use my Master Ball on random legendaries before, but now I just don't tend to use it. I'm always thinking that, sure, I could use it to catch a particular Pokemon, but do I really need to? So I just end up saving it, and saving it, and saving it...
The main times I remember using mine were on Raikou in Soul Silver (mainly cause it was a roamer, I spotted it before Entei, and the purple on the ball went well with the purple on its back haha) :)
Also on Zygarde on X because by that time I'd caught all the other legendaries in the game.