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GIRATINA. I tried to catch him at least ten times, each time getting him red and throwing ultra balls until he defeats all my pokemon or suicides using struggle. Eventually I gave up and used masterball... i could get enough from my emerald anyway, so wasn't a big loss.
I remember Heatran and Regigigas refusing to stay in the Dusk Balls and I had to use like 50 of them to catch them.
When it comes to the roaming Pokemon, the legendary birds in Platinum were much harder to catch than Mesprit or Cresellia because all three had Roost. I was livid when they used it on me and just imported Master Balls over from Leaf Green to catch the suckers.
I remember when I went to face Giratina in platinum i forgot to buy more ultra balls. So he was almost impossible to catch with only 5 ultra balls. I finally managed to do it though.
I found all the other legendary's easy to catch, except for Reggiggas, I found it the hardest because you had to acquire the 3 other pokemon before. But I eventually caught him! :D
Cresselia, as I used the MB on Mespirit so I could comfortably continue with the story. Even with a Gengar mean looking - she still refused to call it quits.
Well to be honest I never caught many Legendaries, I guess I missed all the NDS events >< Except for Victini, I caught it... But it was hell easy. I have to say that the hardest for me has to have been the Nostalgic Mewtwo. Which I no longer have cause I never migrated pokemon... So now since I'd have to get a GBA to migrate pokemon I'm playing all games from gen IV and higher to migrate them all to my Pokemon Black.. Wow.. I jumped off topic there...
Heatran. I got it to low health and I kept throwing Ultra Balls. It went to the point that Heatran ran out of moves and used Struggle. Because of recoil, it killed itself. >:V
Palkia, it was weak compared to most but I just could never get it.
But the hardest I ever faced was Entie, I tried so many times, on gold,silver and crystal never came close. I didn't know how to track to well either, when I ran across it, I never had a move to make it sleep or mean l
Hiidoran, oh great Sky hiidoran (Heatran. Whatever.)
If I calculated right, it took around 600 attempts (so glad I never saved after a round with it and just re-loaded) before we finally got him.
At one point it was at roughly 1-2 HP and frozen, but NO. I think that was a round where it struggled itself to death.
And then one day it decided to just stay in an ultra ball, presumably to irritate me.
Regigas was the hardest for me. It took me 1 hour and I decided to come back later. Then I forgotten where he is and it took me 1 hour too. Finally, I found him. THEN IT took me 20 Ultraballs, after that I decided to use my 2 Master Balls, and finally, I got him.