Yu-Gi-oh is an ever evolving game, with new cards coming in constantly. So Konami has to get rid of certain cards that are dominating the meta, thus making sure the YuGiOh meta doesn't get stale. YuGiOh got their newest ban list a couple days ago, and this article will explain why cards were hit and why cards were unhit (is that a word?
Performapal Monkeyboard - This card was previously limited in the TCG and Konami decided to make this card forbidden. Monkeyboard was one of the remaining Performapal cards that was keeping the deck relevant. This card is literally free search for the deck. You can compare this card to Qliphort Scout, except Scout has restrictions to the card, like you have to play 800 life points and you cannot special summon cards besides Qli cards. This card is also versatile with it's scale; you can keep it as a 1 scale or make it a 4 scale.
Kaiser Colosseum - People are really scratching their heads as to why Konami banned this card. The best that the community can come up with is that the wording is odd and it is one of the best floodgate cards out there. Some people also say that Konami is just too lazy to reprint the card or change it because it is an old spell card, but the debating is still on going.
Cir, Malebranche of the Burning Abyss - Cir is a staple in BA simply because you can Special Summon it almost for free and you can special one BA monster from your graveyard once this card is destroyed. This card was semi limited, but Konami decided to make this card limited in hopes of hitting BA slightly.
Monarchs (Ehther, Pantheism, Stormforth) - Monarchs has been a meta defining archetype since the structure deck was released. The deck does many things too well. Ehther is free deck search with special summoning on top of that. Pantheism was insane card draw and also was able to search, making the card insanely good. Stormforth was also just an insanely good card, allowing you to tribute one of your opponents cards. It didn't matter if the mosnter couldn't be affected by card effects.
Kozmo Dark Destroyer - Kozmos is a deck that floats like none other and can create OTKs. Making Dark Destroyer limited should help heavily, since this is the deck's boss monster of sorts. Also, with Emergency Teleport going to one, this should also help keep Kozmos in check.
Majespecter Unicorn - Kirin - This card was splash-able into any pendulum deck. The card cannot be destroyed or targeted by card effects and it was able to bounce a monster on the opponents side of the field for almost no cost. Overall, this card was just really good and so Konami put it to one.
Beatrice, lady of the Eternal - BA was hiding in the shadows until Beatrice came out. This card made the deck even better than before, and hopefully Konami making this card at one should help. They did not hit Dante, but this might be enough to keep BA at bay.
Pendulum Call - Pendelum Call has similar issues to Pantheism. Discard one to search for two magician pendulum cards. This card can also make your pendelum zone cards float, making your next play pretty safe. This card is now limited.
Maxx C - This card was free card draw and very splash-able, so Konami put it to two.
Thunder King Rai-Oh - Konami realized that this card was not worth being kept limited, so they made it semi limited instead.
Wind Up Magician - Wind Ups have not been viable in quite a while, ever since Konami hit the deck a while ago. So they decided to put the card to two, from one before.
Allure of Darkness - I am honestly not sure why this card is not on the list anymore. It is splash-able card draw that any deck can use as long as there are dark monsters in the deck.
Thousand Eyes Restrict - Konami tested to see if this card would be too overwhelming in the meta again at one, and no one really paid it much attention, so it is back at three.
Gold Sarcophagus - The search form this card is very slow in this meta, so Konami put it back to three.