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I used master ball, I was just not willing to spend the time re-catching rayquazaa repeatedly after hearing the horror stories about it.
Besides that, my team wasn't hideously over leveled since I spent a lot of the game rotating my team around, partly trying to fill my dex, and partly because I did that for X/Y and it made the game seem more enjoyable.
>tfw I'll have no reason to do it again when I finally finish my living dex
