Aipom probably ranks up there as far as difficult catches go for me too. It is also one of my least favorite Pokemon, making it doubly annoying. 
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For me Zubat, imposible to do a good throw. In the wild I ignore them totally, only in Team Rocket final I do it, but with an angry face.
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Zubat continuously jerks around all over the screen as if it’s staggering in mid-air, Golbat lingers too far away to hit with a curve ball (and when hit with a straight throw usually escapes), and Crobat is a little like a blend of both. Sunny Cherrim never stops bouncing around with that obnoxiously cheerful smile on its face and seems to break free from virtually every hit (even razzberried Excellent throws with Ultra Balls).
These exhausted my patience a long time ago, and I almost never waste a ball on them (unless it’s right after I realized that I need to throw away a bunch of items to clear space in my bag).
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Yanma is just as annoying too.
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Cherrim is difficult to catch because it almost always needs several balls to catch.
Those flying mons like Zubat and Yanma are difficult because they move quite alot
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Zubat and Yanma are easy if you use a nanap berry. Kyogre has always been hard for me to catch.
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I always feel like Combee is harder to catch than it should be.
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Zubat is hard to hit, Cherrim is hard to catch
Lugia deserves a special mention since you essentially cant even wait for an excellent
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I say all the starters are hard to catch
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I always use berries and yellow balls on Starters
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Believe it or not, but once I’ve actually had an instant were Abra didn’t flee after it broke out of the ball. But that was just one time out of several hundreds of throws.
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If I’m right Abra has a 99% chance of fleeing, so it IS possible that he doesn’t immediately flee.
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Patrat is a pain to catch as well.
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Almost all high level low iv and practically useless Pokemon. It’s like the game tells you not to catch because it is useless.
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Yeah, but I still try to catch them because I’m stupid.
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I always find low IV’s, whatever the CP. Unless my bag is only one place short of being full, then the first thing I catch is always a keeper, usually because it has great IV’s. 
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I clean out by the hundreds.
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I came to find that Ponyta is very difficult. I was sad to discover that my second Ponyta I ever run across had gotten away. Once I finally catch one, I will name him/her “Wildfire”.