I really can't decide. I know that Amphy doesn't have a great attack, but I don't want my Thunder missing a lot (or learning Rain Dance along with it, because I know it's not worth it) or because of the PP (Thunder Punch is 15, Thunder is 10)
Thunder Punch may be more accureate but it cant Match Thunders Raw Power
Ampharos usually cant be OHKOed or 2HKOed so its not the end of Amphy if he misses
Also Thunderbolt could be an Option, Its right in between them power wise and More Accurate then thunder.
I would recommend either discharge or thunderbolt, if you can get the tm.
The reason is cause Ampharos would be a really bad attacker, and with such a low speed stat, you can't afford thunder missing so much.
I would put thunder on ampharos if it was part of a doubles set with a Pokemon that has drizzle has an ability. Then you get an OP 110 power never missing move on an ampharos with a base 115 special attack stat.
If you have mega, then it would be 165
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