After much testing, I've found that this method works pretty well for me.
 Feel free to change it any when fixing your decks.  As an example, I'll fix
the Water Blast Theme Deck from Jungle.  If you don't know, here is the deck:
Pokémon (24):
4 Poliwag
2 Poliwhirl
1 Seel
1 Vaporeon
4 Eevee
4 Meowth
2 Persian
2 Machop
1 Rhydon
3 Rhyhorn

Trainers (8):
2 Gust of Wind
2 Potion
1 Professor Oak
2 Super Potion
1 Switch

Energy(28):
14 W Energy
14 F Energy

1) Count your cards.  Then have someone else count your cards.  Make sure you
have exactly 60, no more, no less.  If you don't, fix it.  Water Blast has 60
cards, so we're okay here.

2) Determine your strategy.  You'll need to keep that in mind as you fix your
deck.  For example, if your strategy is to power of Wigglytuff and "Do the
Wave", you'll need to include high-HP basics and card-drawing.  Water Blast's
strategy is "to use Fighting and other Pokémon to stall for time while you
build up a Water Pokémon that uses Water Gun."

3) Remove any Pokémon that don't fit your strategy.  In Water Blast, we can
remove 1 Seel, because Seel can't help us stall for time and doesn't learn
Water Gun.

4) Slim down the number of families.  Decks should only have one Stage-2
family!  In rare cases, they can have two provided they have the cards to
make it work.  Next, a deck doesn't need a ton of evolutions.  I've found
decks to work much better if they only have one or two.  In Water Blast, we
have to first decide between the Vaporeon line and the Poliwhirl line.  Since
we will add Poliwrath at a later step, remove 1 Vaporeon and 4 Eevee.  Also
remove 1 Rhydon and 3 Rhyhorn because they're not doing much for us.

5) Take out any Basics with 50 or less HP that you aren't evolving unless you
have a good reason.  I can't think of any really good basics with 50 or less
HP off the top of my head.  If you find a 50 or less HP Basic to work really
well in your deck, keep it.  However, if you don't have a really good reason,
take it out.  50 HP won't last you very long.  In Water Blast, the Machops
have got to go.

6) Take another look at the Pokémon in your deck and figure out how many
you've removed and how many you have.  In Water Blast we have removed 12
Pokémon now have 12 Pokémon left:
4 Poliwag
2 Poliwhirl
4 Meowth
2 Persian

7) Fix your proportions.  Stage 2 Pokémon should be 4/3/2, meaning 4 Basics,
3 Stage Ones, and 2 Stage Twos, or occasionally 4/3/3 if they are extremely
important.  Stage 1 Pokémon should be either 4/3 or 3/2, depending on how
important they are to your deck.  However, at this step you should decide
whether or not you will use Pokémon Breeder for your Stage 2.  Shaun Rogers
wrote a good article about Pokémon Breeder in June which you can find at
http://www.pojo.com/TCGStrategies/June2000/7o.htm.  I would recommend reading
it.  In this case, I think Pokémon Breeder will serve us better than
Poliwhirl.  Remove 2 Poliwhirl and add 3 Pokémon Breeder.  Also add 3
Poliwrath for Water Gun.  Remove 1 Meowth.

8) Have a starter Pokémon.  A starter Pokémon is one who you want to open the
game with, usually a Haymaker Pokémon.  Another good starter is Kangashkan
because of Fetch.  In Water Blast, we have the choice of opening with either
Hitmonchan or Lapras.  I'm going to choose Hitmonchan, Rocket's Hitmonchan to
be precise.  Although he only has 60 HP (I think) Cross-Counter can make your
opponent think twice about attacking, and 50 damage is great.  Of course,
with the popularity of Scyther and Promo Mewtwo, you may want to choose
Lapras.  Either one works.  In fact, I think the best option may be to remove
3 Meowth and 2 Persian and add 3 Rocket's Hitmonchan and 4 Lapras.  Both
cards fit our strategy and can do damage until Poliwrath is ready to finish
up.

9) Eliminate singles.  A single Pokémon, especially if it's important, won't
do you much good.  You have a about a 10% chance of getting it in your
opening hand.  If it's not one of your prizes, you have a 17% chance of
drawing it in the first 10 cards you draw.  Adding more than one of that card
greatly improves your chances of getting it.  Either add more of your single,
or take it out and add something else.  Water Blast no longer has any
singles, so we're okay there.

10) Spread out you weaknesses.  If most of your Pokémon are weak to one type,
try to add a Pokémon resistant to that type, or that the type you are weak to
is weak to.  For example, if you are using a lot of grass Pokémon, many of
them are weak to fire.  No one's resistant to fire, but you can add some
water Pokémon.  Another alternative is to add another Pokémon of your type
with a different weakness.  In the example above, you could add grass Pokémon
that are weak to Psychic, such as Koffing.  Water Blast has Pokémon weak to
Electric, Grass, and Psychic, so we're okay there.

10) Add anymore Pokémon needed.  You should have 11-15 Basics and some
evolutions.  We have 12 Basics, Poliwag, Rocket's Hitmonchan, and Lapras, and
3 Evolutions, Poliwrath.  We're okay here.

11) Add Bill and Oak.  If you are building a stall deck, I would not include
Oak.  I would still include a couple Bills because any deck can benefit from
card drawing.  I would put 4 Bill and 2 Oak in any other deck.  Add 4 Bill
and 1 Oak to Water Blast.

12) Add Trainers that fit your strategy.  I don't have as many general
guidelines for Trainers as I do for Pokémon, because the trainers you'll need
will depend on your strategy.  However, many decks include Super Energy
Removal, Energy Removal, Gust of Wind, Computer Search, Scoop Up/Mr.
Fuji/Pokémon Center, and Plus Power.  I would recommend putting some of these
cards in your deck.  There are many other trainers that are good too. For
Water Blast, add 1 Gusts of Wind, 3 Super Energy Removal,  3 Scoop Up, and 2
Computer Search.  Remove 1 Switch, 2 Super Potion, and 2 Potion

13) Eliminate singles.  A single card won't do you much good, unless you get
lucky.  Either add more of that card, or remove it and use that slot for
something else.

14) Add any more Trainers needed.  I would suggest around 20, although some
decks will have more or less.  Keep in mind that Prop 15 would change this
for tournaments.  Water Blast currently has 20, which is fine.  We're ready
for energy.

15) Count your cards to find out how many slots you have left.  Don't count
the energy you already have in your deck.  So far, Water Blast has 35 cards
in it.

16) Determine if you can make good use of Double Colorless Energy, Rainbow
Energy, Full Heal Energy, or Potion Energy.  Do you have colorless Pokémon or
Pokémon with colorless attacks?  Do you have many different types of Pokémon?
 Do you have need of Full Heals or Potions?  Since most of the Pokémon in
Water Blast use Water Energy, except for Rocket's Hitmonchan.  We won't
include any of these.

17) Determine the remaining energy you need.  For Water Blast, we'll remove 5
F Energy and add 6 W Energy.

18) Playtest your deck and fix any problems that you're having.  I playtested
the new Water Blast, but with one change.  I don't have enough Rocket's
Hitmonchans, so I had to use Base.  Still, I noticed a few things.  I had
some very close calls in which I had only one Basic out and it was nearly
KO'd.  I had some times when it was KO'd.  This happened more often then I
liked.  I also had to mulligan a couple times, and ran low on energy.  The
solution, more Basics and card-drawing.  To kill two birds with one stone,
take out 1 Lapras and 1 Hitmonchan and add 2 Kangaskhan.  I also frequently
had Pokémon with only 10 HP left.  To counter that, let's add PlusPower. 
Take out a Bill, since we have Kangaskhan.  Also take out 1 Gust of Wind, 1
Scoop Up, and 1 Pokémon Breeder.  I found 3 to be more than I needed.  Add 2
PlusPower.  Keep in mind that fine-tuning your deck is an ongoing process. 
After this, play your deck some more and fix any problem that come up.  Maybe
you'll find that you removed too many of a card.  With each expansion pack,
take a look at the new cards in it and see if any of them fit your strategy. 
Good luck!  Now, let's look at the final Water Blast:
 Pokémon(15):
3 Lapras
3 Rocket's Hitmonchan
2 Kangaskhan
4 Poliwag
3 Poliwrath

Trainers(20):
3 Bill
2 Oaks
3 Gust of Wind
3 Super Energy Removal
2 Scoop Up
2 Computer Search
3 Pokémon Breeder
2 PlusPower

Energy (25):
9 F Energy
16 W Energy

Hope you liked this article.  I realize it was rather long.  If anyone wants
to e-mail me, my address is Woof246@aol.com
~Madame Butterfly