If you haven't already read the Beginner's Deckbuilding Advice section, I recommend that you look it over. Some of the points made there also apply here.

1. Staple Cards.

High End Staples (these cards can help every deck)
Pot of Greed
Graceful Charity

Normal Staples (these cards are extremely good in the vast majority of decks)
Monster Reborn
Call of the Haunted
Premature Burial
Change of Heart
Snatch Steal
Dark Hole
Raigeki
Mirror Force
Harpie's Feather Duster
Heavy Storm
Mystical Space Typhoon
Imperial Order
Witch of the Black Forest
Sangan

Low End Staples (these cards are good, but not always necessary)
Torrential Tribute
Magic Cylinder
Nobleman of Crossout
Waboku
Scapegoat
Exiled Force
Sinister Serpent
Jinzo
Fiber Jar
Cyber Jar

2. Experiment with different themes. You can see which decks work, and which ones don't. You just might find a deck-type that's a little more effective than you ever dreamed. In addition, the more experience you have playing with and against different decks, the more you'll be ready to face those decks in tournaments. If you play with and against beatdown all the time, you may be in for a real shock when you face your first Fire Princess, Last Turn, Water, or Hand Manipulation Deck.

3. Use plently of Magic and Trap Removal. I see too many decks that are lacking here. A Feather Duster, Heavy Storm, 1 Typhoon and 2 Dust Tornados (now that Typhoon is restricted) isn't too much removal. As a matter of fact, it's a very good idea in most decks. Heavy Storm and Feather Duster are good for clearing the field. Typhoon's ability to chain to/destroy Call of the Haunted, Premature Burial, Snatch Steal, and Imperial Order makes it very effective. Typhoon is also effective for destroying power-up equip cards when your opponent attacks with the monster. By using plenty of Magic/Trap Removal cards, you can prevent your opponent from getting to use their powerful cards. By not using enough of these cards, you put yourself at the mercy of your opponent's set/continuous cards.

4. Don't use too many Flip Effect monsters. Unless you're running a specific deck that requires certain flip effect monster to be effective, lower the number of flip effects in your deck to 3 or less. In a non-hand manipulation deck, I'd recommend running Fiber Jar and Cyber Jar. Magician of Faith is outdated. The game has evolved to a point where you don't need to use the same Magic Cards again and again because there are so many good cards to use. In addition, it's a liability. There is nothing like watching someone lose a game because their opponent uses Change of Heart on their Magician and takes a game-breaking card from the Graveyard. Choose your flip effect monsters carefully. Use ones with effects that aren't as likely to hurt you if your opponent manages to take the monster with Change of Heart. If the effect doesn't damage your opponent significantly,don't use it.

5. Watch out for power-ups. There is a time to use power-ups, and a time to avoid them. In most decks, you should avoid them. However, there are a few select decks that can really benefit from them. One example is a Gradius Deck. For decks such as that one, you should choose 2-4 power-up equip cards to use. Don't use too many, they burn your hand. Choose only the best equips for the given deck. United We Stand is a very good choice for a Gradius Deck, but Mage Power might not be (Gradius reaquires a lot of cards, you don't always have extras to set). In most other decks, don't use any at all. Beatdown is better without equip cards.