Synergy is how well one card “combos” with another, or how well the two (or more) cards work together as a team. A synergistic pairing of cards usually allows for more consistent gameplay, reducing the amount of luck a player needs to do what they want to do.
Usually, there is a trade-off between how well a card works (once in play) and how much effort is required to put that card into play. For example, we'll take a look at Pokemon that can induce the Burn Special Condition using a Poke-Power.
Torkoal from Unleashed, a Basic Pokemon, has a Poke-Power that can Burn the Defending Pokemon, but only on a heads on a coin flip, as well as only on the turn it is put into play from the Trainer's hand. It only takes one card to get this effect, but its Poke-Power is not reusable, unless you invest additional cards to find a way of returning it from your Bench to your hand.
Houndoom from Undaunted can use the same effect of that Poke-Power every turn, but is a Stage 1 Evolution card, requiring the Basic Houndour to first be played and evolved. This would require the investment of at least two cards, the Basic and Evolution, but provides a re-usable effect.
Blaziken from Platinum guarantees the Burned Condition, no coin flip needed to cause it, but is a Stage 2 Pokemon, needing to get from the Basic Torchic to its Stage 2. This can typically be accomplished either by normal evolution through the Stage 1 Evolution Combusken, or by usage of Rare Candy to skip to Blaziken. Either way, it requires at least three cards to ensure the Burn every time it goes from your turn to your opponents', but reduces the amount of luck required in order to pull off causing the Burn. Jumping the gun a bit, you could say there's synergy between Blaziken's Poke-Power and first attack, Clutch. If one uses the Poke-Power, and then the attack, Clutch goes from being a 40 damage attack that prevents retreat, to one that also requires the opponent to flip two coins, putting two damage counters on the Defending Pokemon for each tails they flip. As you might realize, these two effects work well with each other, seeing how Special Conditions would be recovered from, if that Pokemon could retreat to the Bench.
For some examples of what I would call synergy, consider the Japanese
Leafeon vs Metagross Expert Deck kit, which contained two 60-card decks. Although not perfect, these decks exhibit a greater degree of “synergy” than your average English theme deck. (For this reason, I keep a spare copy of each, using their English prints, as an educational tool at the League I attend, also allowing players to borrow either, so that they may learn from them.) Before you continue reading, I suggest you look over the deck lists.
Let's start with the Leafeon deck. In here, there are a few different combos to be found that increase overall deck synergy.
Leafeon has two attacks. The first does 50 damage for each Special Condition affecting the Defending Pokemon. An attack that does no damage (assuming no Special Conditions) does Leafeon no good, but even causing one condition makes the damage jump up to 50. Tempting, no? Here is where the gears should start turning, if you think about synergy. The next thought would typically be “here is a very cheap attack, in terms of damage done to Energy needed to use it. How can I cause a bunch of Special Conditions on their Defending Pokemon?” That is a very good question. Many decks your opponents could use might have ways of switching their Pokemon; the Bench cures Special Conditions, wasting the time spend to inflicted them. Its second does 30 damage, and induces the Sleep condition, which has a 25% chance of carrying over into the beginning of your next turn. Although the effects are good for its cost, you might imagine it would be more efficient finding ways to Poke-Power up the first attack (and make it the more attractive option to use), relying on the second attack as a last resort for dealing damage.
Fortunately, the Leafeon deck has some tricks up its sleeve to help Leafeon out.
Roserade from Unleashed has a Poke-Power that induces Special Conditions on the Defending Pokemon. This combos well with its attack, which does 20 damage for each Energy attached to it. Not only are you rewarded by its Poke-Power for attaching Energy to it, but also by its attack, which become more powerful the more Energy you attach. A keen eye would realize that Energy Signal also helps out Leafeon, who only needs one Energy to attack; after that initial investment, so Leafeon can use its attacks, any subsequent Energy can be attached to Roserade, causing Special Conditions that boost the power of Leafeon's first attack. The Poison damage between turns further adds to damage their Pokemon takes, even if you don't have enough Energy to attack with anything. Compare this to
Roserade from Supreme Victors. Notice how the increased Retreat Cost and high cost of Poison Seed (as well as the lack of useful Poke-Power) do little to nothing to help Leafeon. This would be an example of a card that does not help the deck's synergy.
Torkoal as previously described has a chance of causing a Burn to the Defending Pokemon, but only when coming into play. Though it combos with Leafeon, helping what the deck wants to accomplish (cause extra Special Conditions so Leafeon can hit harder), it is not very consistent, relying on luck to “hopefully” add more damage, instead of ensuring it. Thus, Torkoal's synergy with Leafeon is weaker than Roserade's is.
How could we further increase the synergy of this deck, with cards not included in this deck? Here are just a few examples, though by no means are these perfect ones.
Leafeon Lv.X: Transforming Leafeon's Fire x2 Weakness to a +30, as well as giving it 20 more HP (at the cost of an increased Retreat Cost), Leafeon Lv.X has a Poke-Power that further increases the rate at which you can attach Energy to your Pokemon. Its attack works in synergy with its Poke-Power, dealing additional damage just for having more Energy in play.
Dawn Stadium: Rainbow Energy puts a damage counter on the Pokemon it is attached to. Why not reduce the cost to nothing when attaching to your Grass-type Pokemon, like Roserade, who can now induce both Special Conditions without taking any harm? This also removes a damage counter any time you put a Grass Energy onto a hurt Pokemon. The only drawback is that your opponent can also use this effect on their Water or Grass-types.
Seeker: Clever use of this card after putting Shaymin on your Bench and moving all the Energy from a damaged Pokemon onto less-hurt ones would allow you to recover a Benched Pokemon on the verge of being Knocked Out, which would drag all cards attached to it down to the discard pile with it. Seeker could even allow you to reuse Shaymin's Energy-moving power. Just remember that your opponent could use it to return an injured Benched Pokemon, or something that has a useful “from-hand-to-Bench” power like the Shaymin has. Seeker combos well when your opponent only has one Benched Pokemon, and an Active you know you can Knock Out, to leave them with no Pokemon left in play.
Broken Time-Space would help this deck get from Basic to Stage 1 in the same turn; given how this deck sacrifices HP for increased offensive power and set-up speed, this could save you a turn that could win you the game.
Skuntank G: The benefits of “free”, consistent Poison, at the cost of also Poisoning any Pokemon that isn't an SP (i.e. everything previously mentioned in this deck). Saves you from attaching Energy to Roserade in a pinch.
I'll delve into the Metagross deck when time permits. I've focused on the Leafeon deck simply because I believe its Pokemon provide an excellent example of synergy.