You hear people complain how Yugioh is broken, and it could be fixed if only they balanced out the game by banning some cards, making new ones, and so on.
I think the game is broken to the core because, unlike Pokemon and Magic, it has no floodgates to control the game. The game wasn't bad when it first came out but now it's cancer. Playing with most decks these days means spending 30 minutes on your Main Phase setting up a field, with battling your opponent as an afterthought, so much it is somewhat like playing solitaire.
I don't suggest adding anything like Energy or Mana cards to the game; they're hideous and clog up a deck. I have other thoughts, only musings, which will probably never be put into practice, but I'm not expecting that anyway. Just a few thoughts on a boring Saturday.
The Yugioh card game in the manga seems to have a pretty answer. You could only Normal Summon 1 monster per turn, set/activate 1 Spell per turn, and set/activate 1 Trap per turn.
All manga Spells work like our Quick Play Spells (you can activate them on your opponent's turn but can't activate them after you set them). The catch is most Spells can't directly protect you or your opponent's monsters from your opponent, so you have to use Spells in a more roundabout way for defense. Traps, however, make solid guards.
Manga Yugioh has a kind of poker element to it. You can Set 2 cards facedown but 1 will be a Spell and 1 will be a Trap and your opponent has to use that implied knowledge to work around your tactics. If you play 1 Spell, you can only set 1 card, a Trap, which could be an obvious ambush or a bluff. Again, your opponent will have to think through their options.
Forbidden Memories / Duelists of the Roses Rules
You can play only 1 card from your hand per turn. You can, however, combine cards in move as a combo, or toss away cards from your hand, and then you can draw more cards until you have 5 cards in your hand again. The rule would work way better if we played the game on a DoR board, as your Life Points won't be so bare. Either way, it makes Yugioh a little more like chess, forcing you to think more deeply, which is nice.
Hosts could hold tournaments where players could not make a deck exceeding a set deck cost. A 700 deck cost limit would really force players to pick and choose among stables like Pot of Greed and Raigeki, while something a 2000 deck cost limit means everything goes. Tournaments with deck costs would most likely be held online since the computer could easily calculate your deck cost for you.
I always found anime duels to be more interesting than real life duels, especially in Duel Monsters, probably because anime characters didn't abuse cards like Raigeki or Yata. Yugi and pals did seem to play under a kind of meta, which is hard to tease out, but I'll try. Anime meta was sort of like this:
-Cards that directly destroyed your opponent's cards (like Fissure, Heavy Storm etc.) were limited to 1, while very cheap cards like Dark Hole and Raigeki were banned outright. The anime put the emphasis on battle, not giant Main Phases.
-Many drawing cards like Pot of Greed and Card of Sanctity were out there but limited to 1. Pot of Greed was tolerable in the anime because people didn't use Heavy Storm and Raigeki on the same turn.
-Most burn cards seemed limited to 1, while "direct damage" cards like Tremendous Fire and Meteor of Destruction were banned.
-Maybe there was an overall limit to the number of cards listed above a player could use; like you could only use 10 such "super cards", so you had to pick and choose carefully what cards you wanted to use.
The banning and limiting of so many overpowered destruction cards meant players had to coordinate their monsters better. They couldn't just stack their Deck with staples like we (kind of still) do. I would say Yugi and pals in Dark Side of Dimensions showed a nice balance between Anime Yugioh and IRL Yugioh.