wait, it took me FPREVER to catch GROUDON in soul silver, he is immune to thunder wave, and if you get his hp down (i use false swipe) he will use REST, and fully heal, then rest again if you dont catch him before he wakes up... i use like 70 ultra balls on him
A non-legendary would probably be either Feebas or Relicanth (in RSE). For some reason it took me in excess of two hours to catch it.
The "legendaries" would be latias/latios (since they keep fleeing) and Rayquaza (since I did not wish to use my masterball to catch it). I was quite lucky with Zapdos (in Leaf Green) though.Caught it with just one ultraball, although it had full health.
I'm not really trying to catch 'em all, so I don't bother with the ridiculously hard ones... But I shall second the note on Skarmory in R/S. Effing low catchrate, effing steel bird D:
I'd figure Feebas to be the most annoying (rather than hardest).
I had no idea feebas was THAT ridiculously hard to find. I never saw one in Diamond, which is finally when I decided I wanted to complete as much of my pokedex as possible, so I just traded for one using the GTS. The most trouble I've had with catching any pokemon is Raikou in SoulSilver. He runs away every chance he gets. Even if you put him to sleep he still runs away. So I was using my Crobat that knows Mean Look to keep him in battle, but then he just uses Roar and escapes. It's absolutely ridiculous. Especially with the effort put into finding roaming legendaries like that. I ended up using a Masterball on Entei, and on Latias in Sapphire. As for all the Legendaries that stay in one place(love those), I go in with a bunch of dusk balls(has a higher catch rate than ultra ball if in a cave or at night) and save right before the battle. That way it really doesn't take a lot of work, just patience.
lol try another trainers pokemon with master ball,i was bored and i tried to catch another trainer's pokemon with a masterball it wont work...IT LIED!!!!!