Yugioh Deck Building

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1. Stick to the 40 card minimum. Well, 41 or 42 is ok. But this is the number one mistake that new deckbuilders make. Many newer players believe that by adding more cards they have more options. In fact, the opposite is true: you have less options. Why? When you're dueling, every single card you draw counts. If you can't draw the right card at the right time, you'll lose. The fewer cards you have in your deck, the greater your chances of drawing the right card. Let's say it's deep into the duel. Both players have gone through a lot of cards and now it's down to a topdecking war. Who has a greater chance of drawing the card they need, the player with 5 cards left or the player with 25 cards left? Some decks also run best with 3 Upstart Goblin effectively making the deck count 37.
2. Don't try to do too many things at once. Pick one central idea and choose every card based on that idea. If a card does not blend well with your central strategy, or is counterintuitive, avoid it. There's probably a better choice. Don't mix ideas unless they actually benefit from each other. For example, there's no benefit from mixing Gladiator Beasts and Lightsworns. GBs rely on having cards in the deck, while Lightsworns mill cards out of the deck. Lightsworns rely on explosive finishing moves while GBs are much slower-paced. Some hybrids are beneficial, though. For example, Lightsworns and DARK Monsters; DARK decks thrive on having monsters in the Graveyard, and using LIGHTs and DARKs together allows the use of Black Luster Soldier - Envoy of the Beginning and Chaos Sorcerer.
3. Monsters are not win conditions. Continuing on the idea of number 2, your central theme should not be "Summon this monster". Aside from Exodia, there is no monster that will outright win you the game. Not the Egyptian Gods, not the Sacred Beasts, not the Aesirs, not Dark Armed Dragon, not Judgment Dragon, not anyone. Monsters, even incredibly powerful monsters, are tools to be used at your disposal. They are not win conditions.
4. Anything worth running is worth running in multiples. This is more true of monsters than spells and traps, but is in general true. Most top decks run all cards that aren't limited in twos or threes. The logic is this: if a card is powerful, you want to draw it more often. If you have more copies, you'll do that.
5. The less conditional a card is the better. This covers activation conditions, costs, benefits, card advantage, everything. The best card is one that is powerful, has little to no cost, generates lots of card advantage, and requires no other cards to be present. Dark Hole is a prime example of such a card. When considering this point, ask yourself "How useful would this card be if it were the only card that I had to use?" or more simply "What would topdecking this card mean for me?"
6. The more versatile a card is, the better. Continuing number 5, a card that can be used against more cards and strategies is more helpful than a card with limited use. For example, Solemn Judgment can be used against all types of cards, making it more useful than Magic Jammer, which can only negate Spells.
7. The more Card Advantage you result in from using a card, the better. To explain this key point, I'll again look at Dark Hole. If the opponent has two monsters, and you have none, activating Dark Hole will leave with the opponent with 2 less cards, and you with only one less card. That generates Card Advantage. Now let's look at the same situation, this time using Lightning Vortex. Lightning Vortex requires a Discard cost, which means it requires 2 cards to play: LV and the discarded card. Your opponent loses 2 cards, and you lose 2 cards. This generates no card advantage.
8. Maintain a proper balance between monsters, spells, and traps. What this means for you depends on the type of deck you're building. Chaos Dragons, for example, rely on milling their monsters to the Graveyard. As a result, they should run more monsters. Gravekeeper's rely on using Spells and Traps to shut down the opponent, so they should run fewer monsters in order to draw more Spells and Traps. Frog Monarchs rely on the effect of Treeborn Frog, so they should run fewer (or no) Traps. To figure out the proper balance, think about what's important in the deck. What does the deck rely on and how should your monster count reflect that? What type of cards would get in the way of your strategy, and what type of cards are crucial to it?
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