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Moltres, definitely. I wasted all of my Ultra Balls on it (twice), with it down to red HP before I managed to catch it. It kept beating my team up, too...
In my experience, Articuno was ALWAYS the easiest one to catch, in FR/LG it always required me 2 or 3 Ultra Balls, even if last time I caught it with the first one :D
Moltres, middle difficult, just for the annoying Fire Spin and then Agility + Flamethrower.
But the hardest for me is Zapdos. With T-Wave, Agility, and Detect, it is a REAL PAIN IN THE ASS!
I think it took me the longest to catch Moltres. I wasted a masterball (!).
But, Arcticuno was the most annoying because it takes SO LONG TO GET TO IT. Seriously.
Articuno and Zapdos were a piece of cake! But MOLTRES! It took me three resets with 99 Ultra Balls to catch it, it was low health and paralyzed, I never want to catch one again...
I don't know why, but for me it was Moltres. It was really easy to get down to low health because of Endure, and I just Paralyzed it after that. Yet, it still took at least one reset each time I tried to catch it. It just wouldn't go inside the Poké Ball.
Moltres!! >O It scarred my Parasect for life!! Without my Parasect, I couldn't land a single status on it and ended up using up all my balls. (Master Ball was in storage, I never use such balls x/)
Zapdos and Articuno were pretty easy to me. I had Articuno paralyzed with a red health bar after an attack from Jolteon. :) Zapdos was nabbed swiftly when Parasect gave a good Spore (that didn't miss for once! XD)
I used false swipe and sleep powder on all three of them, so none of them were really a huge bother, but for some reason Articuno took a lot longer to catch than the others. If I recall correctly I actually had to reset once or twice on Articuno, which I'm sure I didn't have to for Zapdos or Moltres.
I vividly recall my Moltres battle lasting for ages. I don't even know how or why. I just remember using tons of ultra balls, and it like constantly using endure and whatnot.
It was maddening.
Though, in the end, it was mine!