Hi again, it's been awhile since my last article on the pojo, because I've been pretty busy on Starcraft - Battle.net lately...
But getting to the point...

How do people choose the colors in their decks?
Do you just choose the 2 colors that your favorite pokemon are?
I think that's how some people do it...
In my opinion, you really should only decide on 1 color. 
If you have a dual-color deck, make a mono-color first, and then decide on your second color, according to your mono color's weakness.
Such as the following.
 
Original Color                    Supporting Color
Fire                                      Electric
Water                                  Fighting
Grass                                   Water/Colorless (depending on which grass pokemon)
Psychic                               Colorless/Fighting (depending on which psychic pokemon)
Electric                                Psychic
Fighting                              Colorless/Fire (depending on which Fighting Pokemon)
 
Now, if you look at the combinations, you'll see that there are two instances of half-fire decks, them being Fighting/Fire and Fire/Electric.  Which is better?
Neither. 
The way you choose which combination to choose, is simple. 
Choose which color will be your main fighting color.  As in a fire/electric deck, use Fire as your fighter, and Electric to fend off water, since there are no real popular water pokemon that are weak to grass, and you have Scythers for those rare occasions.  In a Fighting/Fire, use Fighting to attack, Fire to fend off grass, if you're using the fighting pokemon weak to grass, but if you're using the Hitmo's...You should go Fighting/Psychic.  When doing these combinations, it's better to have switching trainers, like Switch or Scoop Up, or pokemon of the main fighting color have low retreat costs.  In case you're wondering about those comments "depending on which ___ pokemon you're using"  its like this.  With Fighting, if you're using the Hitmo Family, it's better to use the Colorless pokemon that have resistance to Psy, which the Hitmo's are weak to.  But if you're using the Rhyhorn, Golem, Sandshrew families, use Fire, to fend off the Grass pokemon that your main fighters are weak to.  These techniques are very good against Potpourri, since you're playing their weakness, and you're not using enough colors to make all of the Potpourri's pokemon super-useful.  Psy, if you're using the ghosts that have no weakness, I suggest using fighting to accompany them, since Colorless pokemon will be stomping the ghosts with resistance.  But if you're using Alakazam, Mewtwo, Jynx, etc., try the Colorless pokemon, so you can fend off other Psychics.  As for Grass, if you're using the Poison side of grass, you'd want Psychic or Colorless to ward off the Poison pokemon's weakness, Psychic, but if you're using the Real grass (Venusaur, Venomoth, Tangela, etc.), it's better to use Water to ward off the Fire weakness. 
 
*WARNING* - There is a single weakness to these strategies.  DITTO. He will crush your Weakness controlling abilities, so you'd better have some way to kill off your own pokemon, unless you have a Psychic side to your deck, and you have Promo Mewtwo, which can kill itself in a hit.
 
Hopefully this will change the way you choose colors.
 
        -sleepy dragon
 
sleepyxdragon@netzero.net
 
P.S.
If this helps you at all, and you actually have the chance to pull their weakness on them, email me and tell me!