AzNLeviathan@aol.com
These aren't necessarily in order, just put in the order they come into my head.
By the way, I am not a nut for theme decks, this is , as I see it, just the general complaints of many newbies and non Yu-Gi-Oh players put into a list. Players that are higher up on the Yu-Gi-Oh pyramid realize this, but accept this as a core part of Yu-Gi-Oh, and I consider myself among them.
In the following lists, "category" refers to monsters, spells, and traps.

10. Imperial Order- Leaves the controller with full control of negating an entire category, only having to pay 700LP. Even without paying, it negated at least 1 Spell card, or it took 2 (Spell + MST) to kill it.
Fix- raise the cost of upkeep, or limit its lifespan to a mandatory 1 turn.

09. Raigeki- Obviously banned in Japan for a reason. One of the cards that are the reason for less Theme decks. A number of monsters require that they stay on the field for their effect, such as Fire Princess, and this card ruins it. Not to mention, this card has a potential for 1 (spell) for 5 (monsters) card advantage.
Fix- Only destroys facedown monsters, or only destroys 1-2 of your opponent's monsters.

08. Tribe Infecting Virus- This card, in the current metagame, is a moderately good effect, but nothing truly broken. It does, however, put a stop to theme decks. With 1 discard, this card can have a Raigeki effect for Theme decks which usually have the same monster sub-types. And, it will rarely be killing itself.
Fix- Discard 1 card for 1 monster.

07. Harpie's Feather Duster- Again, anti-theme deck. As any new set is released, if any card is a Continuous Spell or Trap card, its immediately ignored unless the effect is very good.  3x MST, Breaker, and Heavy Storm is still a lot to discourage theme decks that focus on M/T. Not to mention, again, potential for 1 for 5 card advantage.
Fix- Only destroys Face-up or Face-down M/T, or limit destruction capability for 2-3 cards.

06. Jinzo- Of course, this is one of the most controversial cards in the game. While Jinzo is annoying, it does force many people to reduce the number of traps they have to only staple level. This card has the ability to negate an entire category, as well as dominate another category (monsters). This card forces every serious player to limit and change their decks. It is because of this card that 1-Sac monsters and 2400ATK are recurring ideas in this game.
Fix- Make it a cost or payment to negate Traps, such as discarding or paying life.

05. Waboku- This is thought of as a True staple trap. This also is a controversial trap card. Chainable to everything, this card can force your opponent to waste monsters or MST/Harpie's to kill a facedown Waboku, just to find out that you are safe from battle for a turn. Playing this basically means that you get a free passage from 1 turn to your next turn. However, on the reverse side, this card, despite its effect, does not give you card advantage. Your opponent's monsters are still there for next turn.
Fix- hmmm.... is it perfect the way it is? is it?

04. Yata-Garasu- Big surprise. Weak stats and it comes back. Drawing is everything, and this leaves you with nothing. And its very pathetic getting killed by this, because we all don't mind getting beat down to 0LP, but getting pecked 200LP at a time until you're at 0, that just sucks.
Fix- Non-spirit? You can't draw either?

03. Delinquent Duo- I started running out of cards so this was the next on the list. The only real question is, is 1000LP for 2 cards a good deal? I don't see this as extremely broken, even with the current metagame, but this game isnt pokemon, you don't get crazy draw power. Even with 5/6 cards at the beginning of the duel, hands tend to die fast, and this is why this card hurts.  A main reason why Sinister Serpent is considered by many as a staple monster card.

02. Chaos Soldier- hmm... this card is always overshadowed by his cousin, Emperor Dragon, because of its lack of immediate card advantage, or damage potential. This card has to go into battle for its other effect to work, where it can be vulnerable. However, free monster removal a turn hurts. And, a Hayabusa Knight effect for a 3000ATK monster cant be all that good. And of course, this doesn't waste your summon for the turn.
Fix- lower attack? payment cost for removal effect?

01. Chaos Emperor Dragon- what makes this card so good is that it has priority to use its effect. Unless you have Solemn Judgement or Horn of Heaven at the right time, it'll come out on to the field with priority to pop everything. Not to mention, its usually turned into paying 1000LP to do around 3000LP damage. Dealing 2000LP and putting the game into top deck mode, often ruining what strategy and combo your opponent had really hurts. Another important anti-theme card. Themes often require combos or multiple cards, and this card makes you start all over from the beginning.
Fix- hmmm.... Lower attack, less damage per card...... i'm fresh outta ideas...

Oh yea, just a thought...
In Pokemon, many of the broken or strong Trainers (magic) are classified as Supporter cards, in which you may only play 1 Supporter card per turn.
What if Yu-Gi-Oh magic cards were Supporters?
So in essense, you can't play Pot, Graceful, Forceful, and Delinquent all in 1 turn.
Just a thought....