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When the player uses Shedinja against an NPC, it seems that they'll switch their Pokemon if the active Pokemon can't hit Shedinja but a teammate can. In addition to super effective attacks, they seem to recognize leech seed as "can hit Shedinja", but not stuff like swagger and hail. Which other damaging status moves are also recognized as "can't hit Shedinja" by NPCs? Please answer for every generation when Shedinja existed.

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Aren't these damaging weather moves/status conditions (Hail, Sandstorm, and Will-o-Wisp/Toxic) able to hit Shedinja?
They are able to hit Shedinja. That was acknowledged in the question.
don't NPC's have different levels of intelligence? for example, if it was some root 1 noob, they'd only use attacking moves and rarely status. and if they were a tactical trainer(not elite four), they'd try to use a status 1st turn and use a healing item 1 tine when their Pokemon's hp drops below 20%? And then theres the perish song code for (i think) gen 2 where the NPC checks if your pokemon is blocked for them to switch out of perish song's last turn, so if even their arena trapped/locked in, they can switch if your not. And if your locked in and they can switch, they won't. :P
No, the Route 1 noobs don't attack. They only ever use leer. If they knew how to attack, then they wouldn't be noobs. As for the question, I think I'll just ask for the smartest AI in each game.
Hmm, I still wouldn't know this, but I used Shedninja in my both of my 2 Omega Ruby Playthroughs (and in the battle tree) and know how some AI would act:

Trainers like Steven will use whatever's available, his AI prefers to use moves in like order (on shedninja):

 Super effective moves, moves like toxic, switch out to another Pokemon who has previous (will not switch if false), moves like Thunder Wave, moves like Reflect/spikes, moves like metal sound (lowers special defense, so It looks like a win for an AI but doesn't do much in Shedninja's case), damaging moves, damaging not very effective moves, moves like swords dance. If fit were not Shedninja, his pokemon would use moves like swords dance earlier. Their Pokemon will use moves like roost if they have low HP and outspeed the opponent, if they don't outspeed, they still use it unless they have a priority move. I still haven't worked out where protect would go. I know this isn't entirely about status moves, but it shows the order that they think (because typically in ORAS they'll use nearly all status moves, in the order of most effect) That is all I know. :P

Note: Trainers like Watson and most rout trainers will have the same mostly, but will attack sooner than use less useful status moves Example: Wattson has no more Electrode/Voltorb (forget which one), the only Pokemon with super-effective attacks (Rollout), will use a move like spark over thunder wave.

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