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I have no idea what Mesprit's problem was; just get in the flipping pokeball already! :P
Regigigas I caught fairly easily, as well as Cress/Gira/Azelf/Uxie. Heatran didn't take that long either, compared to Mesprit. Since when can Pokemon escape while they're sleeping? Lame!
Palkia was probably everybody's easiest catch by the looks of the votes...it was actually easy...Giratina and Mesprit is probably everbody's hardest....well most people that is...
Ah man, I was playing Diamond awhile back and I was to the point where you catch Dialga.
I walk up to him and proceed to battle that when it hits me. I haven't saved since a badge ago and I only have one pokeball.
I think "oh great! I don't even get to catch this guy man whatever."
So in vain I throw my only pokeball at it (at full health) and apprehensively waiting for it to fail to turn off my game, but to my surprise the pokeball sealed and I captured it!
Well anyways Giratina was my hardest, at least 10 pokeballs (hoping to have the same as dialga) and 15 ultra balls
I'd have to say Dialga because I was completely unprepared, and got worn out from the previous battles, and was just like, 'What the....', then realized what was going on. All of the other ones, I was prepared for, and knew what to expect.
Azelf was annoying. Nasty Plot.
This was the first time playing Pearl, though.
Now when I play, Regigigas and Giratina are my Rings of Aggravate Monster.
Everyone was super easy for the most part. I ended up using the Master Ball on Mesprit because I was impatient, but Cresselia was a ***** to catch. And it took absolutely forever for my girlfriend and I to catch Heatran. We either kept killing him or running out of balls. It was ridiculous.
It was Giratina but I found it with ease. In Platinum it's hell easy (two Ultra Balls at low HP). In Pearl it took me like 30 Dusk Balls plus a few more when it were at red HP and on my last Ultra Ball I caught it.
..The hardest Pokemon to catch the traditional way has to be the Legendary dogs from G/S/C. Hands down.
Tough little critters..
Edit: I know we're speaking of Diamond and Pearl, but nothing has ever been as difficult to catch as those dogs. Entei was especially the most headache-worthy.