It has everything to do with strength to weight ratio and lever length. Just like anything else we do against gravity, the heavier it is the harder it is to lift. In this case what you're lifting is your body weight. But, leverage has a lot to do with it too. People with longer long bones (arm and leg bones) will typically have more trouble with pull-ups that a person with shorter limbs. So if you've got long limbs and you're not model thin... You get the idea.
This is why most gymnasts are more compact looking. Shorter levers mean you easier work to move those long bones when doing body weight based movements that require power.
Someone else mentioned grip strength and this is very important too.
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