When I played Ruby back when it was the newest game, I had heard that Latios/Latias was even harder to catch then Rayquaza, and so it was best use the Master Ball on them. So, I did that, and resolved to find some other way of catching Rayquaza. My solution ended up being to freeze it, stall for as long as possible, then use a Timer Ball. 😂
Other than that, I think the only time I've used a non-hacked (*coughMissingnocough*) Master Ball was on Mewtwo in Gen 1.