Can you over pay retreat cost? I mean like if you wanted to get rid of a Darkness Energy from a free retreat pokemon, could you discard the darkness anyway when you retreat?
If a Raichu (or whatever) does Agility and flips heads, does an attack that would do damage to benched pokemon, or some other effect that does NOT do damage or something to Raichu work?
Yes it would, while all attacks are considered against the defending Pokemon (which is why something that prevents attacks would stop it in this case), Agility only prevents the effects of that attack if they affect Raichu only.
It has been ruled that W/R does not apply to the bench unless specifically mandated by the card. Period. That is a meta-game rule. It was never intended that the W/R would apply to the bench unless specifically stated. Yes we do know that some Pokemon say not to apply W/R to the Bench. [But] if it doesn't say then you wouldn't apply Weakness and Resistance (the default for benched Pokemon is to NOT apply Weakness and Resistance). This has been verified.
If Wooper uses Amnesia on Scyther's Slash, then Scyther retreats for another Pokémon, then that Pokémon [is Switched] for Scyther again, can Scyther use Slash?
Amnesia references the defending Pokemon, when that Pokemon is benched the effect ends.
If your Pokémon has been Smokescreened on the previous turn, and you choose an attack that requires you to do something (such as discarding Energy) in order to use the Attack, do you pay the attack costs before you flip for the Smokescreen Effect?
Yes before, you still attempt the attack; the Smokescreen might just stop it from having any effect.
When you use a Trainer that requires you to shuffle your hand into your deck does that Trainer get shuffled back into the Deck too or does it go to the Discard Pile?
No, the trainer that you play doesn't go back into your deck. {When you played it, you put it down on the table. It is no longer in your hand]