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We wouldnt recommend it for the rare Pokemon cards in your collection, as this method of storage wont guarantee that your cards are fully protected, but for storing the low value bulk cards, its perfect
The other option is to take advantage of the direct damage, which is good in its own right to either finish off a damaged character or get them within range to be banished but also works with the likes of cards that benefit from being damaged - such as Scroop, Backstabber - that benefit from healing damage, like Rapunzel, Gifted Artist, or from damage being dealt: like Beast, Relentless.
Agree with ya in the Latias-latios, brother-sister thing
Commander has proven to be a great pairing if not the best
For instance, for Pikachu, you will need a rich yellow for its fur, red for its cheeks, and black for the tips of its ears