I would say Mewtwo cause it has the lowest catch rate in the game I think. I usually capture legendary pokemon in regular Pokeballs
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I remember trying for MONTHS to capture Suicune on my Firered.
Even after paralyzing and getting it to the red, that stupid thing would break out on the first try and escape! >.<
Moltres, without a doubt. Took me multiple tries.
I got lucky catching Zapdos in my first few balls(wut), Articuno wasn't too bad and Mewtwo took just under 45 minutes of me slapping my balls into him.
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Aside from the Legendary Beasts, I had a tough time catching a Larvitar. I would find so many of those things, but I could never catch one unless I weakened it, which I usually couldn't do since my Pokemon were too powerful for that. I finally got one after using a Marowak's False Swipe, but it still took several Ultra Balls to get the job done.
Definitely the 3 birds. It was annoying.
Latios/Latias for Pokémon Ruby/Sapphire, 9 years have passed and I still haven't caught Latios. It's on 1hp and the Ultra ball shakes once and then it bursts open
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The legendary dogs. As i chose Charmander most of the time, that would be Suicune. The legendary birds were hard to catch too, especially Moltres. I always saved my Master Ball for Mewtwo so he wasn't much of a problem. Oh yeah, and trying to catch an Onix with a pokéball always was a pain in the rear. >.<