For the tournament player, Side-decking is a term almost all know, yet fewer seem to understand its implications and functions. I look through many deck lists, and see several cards in the Side that I feel either should not be there or are best served as other cards to help take down other match-ups. It causes me to wonder if people truly know what they are doing when making a Side. Here, I will strip away the mystery.
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First, you need a deck. When your deck is finished, tested, and consistent in fulfilling your strategy, you need to prepare a Side.
Some seem to think the Side Deck is meant to help slice advantages by Meta decks. This is somewhat true, but not entirely. The Side Deck is meant to help you crush the advantages of the match-ups that really hurt you. For example, if you run Six Samurai, mass monster removal via effects or simply Anti-Meta Stun cards like Thunder King Rai-Oh are a real problem.
In the article
The Basics of Good Deck Building, Pox Equestria mentions that after you have finished constructing your deck that it is important to take notes on what decks your facing, the results of your game, and the strengths and weaknesses of both decks during that game. This is where your Side Deck becomes clearer.
Take a look at your notes and consider the strengths of the types of decks that would be considered a bad match-up for your deck. When building your Side Deck, consider those strengths because the Side Deck is there to help you against decks that are a problem for yours, not just what you think you will be facing the most.
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Second, think upon the weaknesses of such a deck that can compliment your strengths. All of the Six Samurai are Warrior-type. All of their monsters are different types. There is a single card that can take 2-3 slots in your Side just to help against this match and any deck that revolves around playing different Types of monsters: Rivalry of Warlords.
This card forbids players from controlling more than one single Type of monster. It even wipes the field until each controls only one Type. This can be devastating if they have a face-up Thunder King, Doomcaliber Knight and King Tiger Wanghu on their field.
Now, they tend to have plenty of face-up backfield. The Six Samurai - Kamon can take a single slot in your Side to deal with all of that. He is very easy to retrieve with all the Samurai deck search cards. Kamon will also help with Gravekeepers or any deck that likes face-up backfield.
Finally, you need to think on what they might side against you. Many side in Kinetic Soldier or Puppet Plant. While Puppet Plant is hard to stop, you can do so by Siding 2-3 Dimensional Fissure. Puppet Plant cannot be used when that card is in play. For Kinetic Soldier, Main-decking or Siding 2 Dimensional Prison can get that threat out of the way easily. Finally, Siding 2 Smashing Ground can deal with Thunder King Rai-Oh when they drop it their first turn.
In summary, save slots for the matches that hurt you, not the ones you go even with or just plain annihilate. Unless you are using Samurai, then you need 3 Kinetic Soldier in Side to give every possible advantage against another Samurai player. Additionally, try not to seclude slots to one match-up only.
For example, if you want to rock Plants and Samurai both, side in Chain Disappearance. Plants lose their Tuners forever. Samurai lose Kagemusha forever. No more Synchro problems. This also deals with all the other little monsters that cause trouble in all match-ups.
Try to keep your Side as malleable as you can so that you can Side as hard as you can, every time you run into something unfavorable.