Ugh! Get into my Pokéball, you!

[Sun]

As far as non-legendaries go, I've always had trouble with Skarmory and Onix. Both have surprisingly low catch rates for the point in the game you first encounter them (especially Onix, which usually appears right after you pick up your first Great Ball but before you can buy them in shops). In almost every game I have used up my entire stock of Pokéballs the first time I try to catch one or the other.

Red Gyarados was also very tough for me, and I didnt even catch him. I also found Togekiss to be very hard to catch in my randomized nuzlocke. No matter how low it got and how asleep it was, it would not get caught. Eventually, I was forced to just faint it.

I second that Skarmory, Whether we're talking about SoulSilver or RSE it's a hell to catch them.

Both Togekiss and Skarmory have lower catch rate than the Rayquaza from Omega Ruby and Alpha Sapphire, with Skarmory as the lowest among the three mentioned Pokémon.

 

[Berserkers]

The Pokémon that proved to be the most difficult to catch for me was Metang in the Giant Chasm area in White 2. Not only did it cost me a ton of in-game cash on Quick Balls and Ultra Balls (both of which were ineffective), but it also was able to defeat my whole team multiple times. x_x

I was finally able to catch one, but it truly was a challenge. (Metang's catch rate is equal to that of most legendaries).

 

[AJusa]

I hate catching good ones :(

 

[Pendraflare]

Aipom have been like this before. Once when I was doing a Wedlocke in Platinum (back in 2013 while I wasn't as experienced, NOT the one I did this year) one ran me out of Poké Balls completely. Then just to rub it in my face, it wouldn't let me run away for two turns.

And Cottonee can be stupid annoying to catch - once in Black 2, I had one on really low HP, and it broke out of almost all my Poké Balls. From what I saw on MetalKid's catch rate calculator, it should have had at least an 80% chance of catching with the conditions I had it at, but over half the 10+ balls at it I threw had one shake at most.

 

[Sun]

Aipom have been like this before. Once when I was doing a Wedlocke in Platinum (back in 2013 while I wasn't as experienced, NOT the one I did this year) one ran me out of Poké Balls completely. Then just to rub it in my face, it wouldn't let me run away for two turns.

And Cottonee can be stupid annoying to catch - once in Black 2, I had one on really low HP, and it broke out of almost all my Poké Balls. From what I saw on MetalKid's catch rate calculator, it should have had at least an 80% chance of catching with the conditions I had it at, but over half the 10+ balls at it I threw had one shake at most.

Aipom is understandable, as it has a Capture Rate of 45, which is exactly the same as Rayquaza in OrAs! {XD}

 

[Hiatus]

If we're not trying to mention any legendaries here, I'll likely have to go with Relicanth, specifically in Ruby, Sapphire, and Emerald. I needed this Pokémon in order to capture the Regi trio, but capturing it was... an extremely time-consuming task. I've lowered its health, put it to sleep, and so forth, but regardless of how tough I tried, it still found ways to break out.

 

[DraconianWing]

Rayquaza in Ruby. Unlike Emerald, the Lilycove hideout becomes inaccessible after a certain point in the game (I don't know when exactly, maybe after battling Groudon), so as a result I missed the chance to get the Master Ball. The strongest Pokemon in my party at the time was a level 70 Aggron, which was able to take about 5 Outrages before fainting. It took countless restarts over the course of a few days to finally capture it, since it would always end up using Struggle and fainting.

To put things a bit better into perspective, it was brought down to red health with Paralysis every encounter. Lati@s comes at a close second, though you spend more time tracking it down than actually battling it.

 

[Geltza]

When I was trying to unlock the Regis in Omega Ruby I remember Relicanth giving me a bit of trouble for some reason! Just wouldn't get in the dang ball.

 

[Dedenne1]

Skarmory in Emerald just uhh so many pokeballs wasted! I didnt even catch one it took out everyone in my team before i could chuck all my great balls.

 

[starseed galaxy auticorn]

omfg YES. Too many times have I actually ran out of pokeballs because of the impossible to catch normal pokemon! DX

 

[CountessGardevoir]

Nearly everything in ORAS

 

[PageEmp]

The most recent case of something that could not stop breaking out of my balls was a Girafarig in my Plat run. It severed some major damage onto my gang, and it finally came in....to my last ball(my 8th ball.) and then it was modest, and probably had a decent characteristic. But was it worth it?

And after stocking up, I then got a Chatot. It escaped from my quick ball, and then every ball after that. I gave up on him, solely because I didn't want to waste my balls, and if I stayed, I would have lost a teammate.

 

[Caite-chan]

I think for me it would be while I'm trying to catch a shiny. You just want it in a ball but for me most of the time they pop right out. And the worst part is you don't want to beat it because then you'll have to sit in the corner and cry. I try one move and pray it doesn't faint.

 

[Shiro]

Chansey in the Safari Zones. ;; I'm not sure I honestly ever caught one? And also when I was veeery young and playing Gold, I had a lot of issues catching Aipom. And then when I finally caught it I got so excited I... dropped my Gameboy and the batteries came out. So I had to catch it again.

I can't think of any in more recent years aside from the legendaries, though.

 

[Tora]

I caught a Metang in a friend safari yesterday, because I still needed Metagross for the Pokédex. It was a pain. I had it on literally 1 HP with False Swipe, since it didn't have any recoil moves and I put it asleep over and over again. I finally caught it in a Timer Ball after I went through half my Ultra Balls.

On the other hand, I caught Moltres earlier this week, with a synchronizer in front. I got a Modest one with good IVs on the first try, and it was caught in the very first Premier Ball I threw just for the heck of it, even though I hadn't even put it to sleep yet!

 

[nookingtons.com]

YES. I have to agree with all the Abra comments. Abra is the WORST.

 

[Kikaito plush]

Dratini in the Safari zone in Leaf green.

 

[magicalgirlj]

Mawhile in Soul Silver- It was swarming one day, so I went to try to catch one and it would not stay in the dang ball, it took me several tries even with Thunder Wave. And it only took me two ultra balls to catch Xerneas(sorry if that is a typo).
I got a Beldum through the GTS on X. Thank goodness they are genderless so you can breed more

 

[Juno]

Quite a few, since I just have terrible luck in general, but Onix comes to mind first as I've run out of Pokeballs trying to catch it several times. :c Threw eeeverything I had at it.

 

[Khoshi]

Abra.

It's the reason I absolutely gave up on playing through Gen I. Can't catch the bloody things. Don't care if I'm adding to the Abra pile, I just hated trying to capture it. Hated it so much, I vowed never to catch Abra, and to instead KO them immediately.