I agree, it's better to batlle and have an epic catch than using a masterball. I prefer to use the masteball as a last resort tool. sometimes is meaningless when you catch a shiny with a masterball without effort. A shiny is more valuable when you catch it the normal way.
But what to do when you catch the shiny so fast with another type of pokeball, it sometimes happen, and there's also the quick ball that make catches a little more easy.
Thinking of this has made me think of something, don't you think it would be interesting to catch a shiny legendary with pokeballs of normal catch rate, like the heal ball, luxury ball, pokeball, etc.