The manga and the anime are quite different indeed. The anime duels never played the same as either the manga duels or the OCG/TCG which came afterwards. Yugi (Atem/Yugi) is much more skilled in the manga.
Only in the anime in the last episode, it was shoehorned-in last minute the magical handwave to explain how he pulled the card he needed in the anime.
The anime added a whole metric ton of cards to his deck that never existed in the comic, because Konami was trying to sell trading cards, which resulted in his deck appearing to be a 300-card pile of crap that didn't have a single strategy.
In the comic, Yugi's deck DID actually have a control-based strategy. Largely focused on spellcasters, fiends, and warriors, his duels were much more consistent and thought out, and he often won through knowledge of the rules, forethought, and clever plays. He never "cheated" in any of his duels. If he got the card he needed, it was luck. The game, no matter what the version, is 50% skill/50% luck.
In other words, Manga Yugi didn't need the plot armor: "The Superpower!" because he had a solid deck recipe and strategy.
So, the whole "destiny draw" thing was never mentioned in the comic, never shown in the comic, and no-one, especially Ishizu, never even theorized on it in the comic, because it never existed.
You could make an argument for Anime Atem because of his destiny draw that he's not really skilled and it's just plot armor. But anime duels were always played with a skill/deck draw power combo. It's literally explained in the anime that if you have a close relationship with you deck, you will draw the cards you need more often, even going as far as knowing that your deck will supply you with the card you need at a specific time.
Yugi/atem has a close relationship with his dark magician, kuriboh and dark magician girl; they help him by making him draw the cards he needs.
This is called "believing in the heart of the cards" and is the most important plot point of the first anime series. Not just that, it's a skill as well. One that can be trained/learnt. In GX for one episode, a guy actually trained in the mountains to be able to draw any card he wanted. In GX, another guy had to sell his soul to the grim reaper to slash-draw.
Dark Yugi has lost three duels in the manga, and five in the anime along with Yugi. Yugi by himself has lost two additional games in the manga. Yugi (Dark Yugi/Yugi) is the type of protagonist that wins a lot so when he loses, regardless of circumstance, it serves as a character development moment. Except his losses actually do this, unlike the sequel series.
Yugi Muto: 34 wins, 05 losses, 01 draw, 04 no result shown
Jaden Yuki: 78 wins, 05 losses, 03 draw, 10 no result shown
Yusei Fudo: 52 wins, 01 loss, 00 draws, 10 no result shown
Yuma Tsukumo: 54 wins, 11 losses, 01 draw, 07 no result shown
Yuya Sakaki: 39 wins, 05 losses, 01 draws, 12 no result shown