The counter system is not a new idea. It’s also something that Konami tried with Turbo Duels. A counter system helps slow the game down because counters act like resource costs such as mana. Then, players need to pay a certain amount of counters to summon or activate.
However, these ideas actually disrupt and break combos. One of the important things of Yugioh is that you can activate or summon a card as soon as you draw it. If you had restrictions, it would break several decks and ideas. Rather than limit the summons or activations, it’s better to limit the number of cards on the field at the end of each phase. There is a idea that’s already implemented in the game which you can try called “Enki Duel”.
Try it in the game.