Deck Building 102
Now I will discuss the choice of Pokemons. There's a few basic rules of Pokemons that usually apply, though not always. First, basic Pokemons are generally weaker then evolved Pokemon. Second, most of the best Pokemon powers come from Stage 2 Pokemons like Rain Dance and Damage Swap. Just because the most powerful Pokemons are Stage 2 doesn't mean you should put as many Stage 2's in as possible. The two basic Pokemons Hitmonchan and Electabuz are stronger then a lot of Stage 1 Pokemons, so never underestimate a basic Pokemon.
You should generally have 12-14 basic Pokemons in your deck. This will lower the percentage that your opponent will get to draw extra cards because you failed to draw a basic Pokemon in the opening round. You may choose all strong basic Pokemons, or a deck based around evolved Pokemons. This article will go in more depth about evolved decks.
I define a Major Pokemon Tree as the entire evolution line of a Pokemon. For example, Bulbasaur, Ivysaur, and Venusaur make up a tree. The reason it's called a tree is that you should have one more Stage 1 Pokemon then you have Stage 2 Pokemons. You should also have one more Basic Pokemon then you have Stage 1 Pokemons. An example, 4 Bulbasaurs, 3 Ivysaurs, and 2 Venusaurs make up a tree. There are always exceptions to the rule, but this is generally the rule you want to follow.
A Minor Pokemon Tree consists of a Basic Pokemon and a Stage 1, but no Stage 2 Pokemons. Evolved Pokemons should always be in tree form. A good example of this is 3 Magikarps and 2 Gyradoses. Pokemons will 3 evolution stages generally have a weak Stage 1, so avoid something like 3 Squirtles and 2 Wartortles without a Blastoise.
Your deck should have no more then one Major Pokemon Tree. Having two Major Trees make if very difficult to bring out the cards you want. For example, NidoQueen seems to fit very well with NidoKing, but having two Major Trees make it very difficult to get both out at the same time. You should decide on one Pokemon Tree you really like, and stick with it.
The rest of your Pokemons should be to assist the Major Pokemon Tree. They may consist of strong Basic Pokemons or one or two Minor Pokemon Trees. Gyrados helps Blastoise well because Gyrados has a different Weakness then Blastoise. You may not decide to have any Stage 2 Pokemons, but you should always keep in mind that your Pokemons must work together as a team. A handful of Scythers will help your Electrode Tree, because Scyther is resistant to Fighting which Electrode is weak to.
Variety may make interesting decks, but it also makes for weak decks. Just like the Gameboy game, you really shouldn't have more then 6 types of Pokemons in a deck. Instead, you should include multiple copies of one Pokemon to increase the chances of you drawing the card. The fewer multiples of a Pokemon card makes you depend more on luck, while four of a card greatly increases your chances of drawing the card.
Anyway, choosing Pokemons is a big part to deck construction. Try not to under do it, but much more importantly, don't over do it. The more Pokemons you have, the less space you have for trainers.