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How much do you care about abilities in the main story?

Depends on the ability. Usually catches four and takes the "best". Weighs ability, nature, and stats (relative to each other). Examples:
  • Hitmonchan: Iron Fist versus Keen Eye. Will take any Iron Fist Hitmonchan over one with Keen Eye, even if the IVs and nature are terrible. Uses Iron Fist all the time. May go beyond the four catch rule and take the first one with Iron Fist.
  • Pyroar: Rivalry versus Unnerve. Prefers Unnerve for being less swingy. Chooses on IVs and nature first, though.
 
I think abilities are very important. As early as gen 3 pick up was one of those abilities that I just needed to have. Especially in Ruby and Sapphire where you have a higher chance getting high tier items like full restores and PP ups. Later gens would interest me with abilities like intimidate on Luxio/Luxray and Gyarados, water absorb on Poliwrath, No Guard on Machoke/Machamp, and own tempo on Slowking. Whether these abilities blocked a specific attack or status aliment, gave me free items, a free stat buff/debuff, or made moves never miss, I would try to go for these even if I have to recatch the same Pokémon in the hopes of getting that desired ability.
 
I'll almost always choose an ability before catching a Pokemon, unless both abilities are useless for the moveset I'm planning for.
 
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