Eh...yeah, let's start by dropping the ones that really have no place whatsoever in a serious deck:
Baby Dragon
Black Pendant
Black Skull Dragon
Dark Blade
Dark Eradicator Warlock
Dark Magician Girl
Exarion Universe
Familiar Knight
Fusion Gate
Gearfried the Swordmaster
Gilford the Lightning
Goddess with the Third Eye
Lightning Blade
Mass Driver
Mystic Box
Rare Metal Dragon
Red Eyes Black Dragon
Release Restraint
Thousand Dragon
Tribute to the Doomed
Warrior of Zera
Honestly, a lot of the cards listed here are just plain bad. First off: Thousand Dragon. Do you seriously intend to go through the bother of assembling three specific cards (Baby Dragon, a fusion substitute, and something to fuse with them), all of which are only present in single copies within this deck, just to get out a monster with no effects that can only manage a draw against Jinzo or a Monarch? That, good sir, is disastrous from the vantage point of card advantage, and I assure you that there are easier and far less expensive ways to get far better monsters out there which don't include adding a worthless vanilla to your deck. Second, Release Restraint: does running a card that is only ever useful if you've also managed to draw into that one other card in your deck and gotten it out on the field (And requires you to risk drawing into a third card which is absolutely useless for anything except discard bait until you've drawn into the afforementioned two) sound like a good deal to you? I hope not, because it really, really isn't. The odds of you even pulling this maneuver off against a competent opponent are diminutive, and even if you do the payoff is really nothing to call home about. Familiar Knight is just plain outclassed by Marauding Captain. (Who gives you (and only you) that free summon without needing to suicide into something first and can also help lock down the field if you're running a committed warrior theme), Dark Magician Girl is just a horribly subpar tribute monster who usually gets run over even by non-tribute monsters (Giant Orc, special summoned Cyber Dragon or Commander of the Six Samurai, etc.) and doesn't have any useful abilities to compensate for its pitiful stats, and speaking of horribly subpar tributes: Red Eyes really takes the cake here. A two-tribute vanilla with stats that would be subpar even on a one-tribute vanilla? Uhh...you might want to rethink that choice. Unless you're running B.Chick, there's really no point with this one, and even then Blue-Eyes + Kaibaman basically trumps that combo anyway. And speaking of Blue-Eyes...don't even think about polymerizing for Ultimate, let alone running the basically guaranteed dead draw that is Shining Dragon. The only things Blue-Eyes has going for it are being the strongest vanilla monster in the game and some minor support in the form of Kaibaman and Burst Stream of Destruction, and really; that's not all too hot when one Brain Control, Soul Exchange, Smashing Ground, or one of the countless other monster removal methods can tear down all your hard work. Just assembling three Blue-Eyes in your hand is a futile endeavor (Trust me, I tried that to amuse myself while leveling up in Spirit Caller; not even the most tedious drag-out-the-battle opponents out there allowed me enough time to find all three, let alone something to fuse them with too) and fusing it with Future Fusion + Dragon's Mirror is just pointless since Five-Headed Dragon is a stronger and more flexible choice. :\ Warrior of Zera is really not worth even considering unless you plan to run some obscure deck that exploits Mazera DeVille, because on its own it's nothing but a wimpy vanilla (Basically trumped in every way by Gene-Warped Warwolf, Insect Knight, Gemini Elf, Vorse Raider, Mad Dog of Darkness and countless others). The only thing Rare Metal is good for is really some sort of combo-action with Hidden Soldier or A Rival Appears! (Activating Hidden Soldier and Torrential Tribute in chain is actually a pretty fun maneuver) and even then the benefits are sort of questionable because it's such a low-utility card. Mystic Box and Tribute to the Doomed are both bad for monster removal because they hurt your card advantage (Tribute to the Doomed is two cards from your hand (One for the activation, one being the spell itself) for a single monster on your opponent's field and Mystic Box is even worse because you end up losing a monster from your field. This could be exploited if you had something that you'd like to plant on your opponent's field, but you don't. :\); Smashing Ground, Fissure, Shield Crash, Nobleman of Crossout and Hammer Shot are all superior choices for monster removal. Dark Eradicator Warlock's effect is strong, but you'd really need a deck dedicated to Normal Spells (and capable of playing a lot of them in one go) to make proper use of it; it's definitely not something you can just slap on and expect to have use for. Similarly, Dark Magician just for the sake of Dark Magician (and yes, I know you have skilled but that alone doesn't cut it) just isn't worth the bother. It's a nice choice if you want to fuel Deck Destruction- or Eradicator Epidemic Virus, though. Kuribohs are cool, but only if you have The Flute of Summoning Kuriboh to make them a special summon, which you don't. Finally, Mass Driver is only good for very specific purposes. (Typically in obscured decks like Clockwork where you can prevent yourself from being outdecked (or finish off an opponent who has paid too many LP costs) by tossing Outstanding Dog Maroon at them again and again). As for the rest of the cards on the above list...they're basically all overshadowed by so many better replacements. T_T
But yeah, start by figuring out a clear win condition for your deck and build on that. Also, if you want to run any of those three types you mentioned, try focusing on the good cards among them, stuff like:
Dragon
Armed Dragon line (Requires a dedicated deck)
Different Dimension Dragon (Sort of...)
Exploder Dragon
Five-Headed Dragon (Basically the reason we want to run dragons in the first place)
Horus Line (Requires a dedicated deck)
Masked Dragon
Spear Dragon
Twin-Headed Behemoth
Spellcaster
Apprentice Magician
Breaker the Magical Warrior (one of the most splashable cards ever printed <3)
Crystal Seer
Dark Magician of Chaos
Magical Marionette
Magician of Faith
Old Vindictive Magician
Royal Magical Library
Skilled Dark Magician
Warrior
Amazoness Chain Master
Amazoness Swordswoman
Armed Samurai Ben Kei (Requires a dedicated deck)
Command Knight
D.D. Assailant
D.D. Warrior
D.D. Warrior Lady
Destiny Hero - Dasher (Requires a dedicated deck)
Destiny Hero - Diamond Dude (Requires a dedicated deck)
Destiny Hero - Disc Commander
Destiny Hero - Malicious
Exiled Force
Freed the Matchless General
Great Shogun Shien (Requires a dedicated deck)
Marauding Captain
Six Samurai set
Spell Striker
Strike Ninja (Requires a dedicated deck)
Warrior Lady of the Wastelands
Not at all comprehensive, but all of those should be good. You really need to find a set of cards that work well together, though, and typically this means going outside the boundaries of a specific type. =O Also, you'll typically want to have as many copies of your key cards as the rules allow to maximize your odds of drawing as well as a lot of support cards capable of finding them; the better your deck is at giving you extra draws and searching out specific cards you need the better your chances of winning consistently will be. You'll also want to keep the deck card count as close to the allowed minimum of 40 as possible to maximize the probability of drawing whatever card makes your deck tick (This rests on the simple mathematical fact that the probability of drawing any given card is the number of copies you have in your deck divided by the total number of cards in your deck). As a rule, it should be 40 cards unless you've got a brutally effective search and/or draw engine in there. You might also want to keep count of how many cards of each type (In this case referring to Spell, Trap, or monster; not monster types, though you might also want to distinguish between tributes and non-tributes in the deck) there are within the deck since it's a good way to check if you have a healthy balance between the three (and thus don't run the risk of drawing into hands with only support cards without monsters to support or only monsters with no spells or traps for support). :3
