I dont know which system im going to use but the actual card game will be played on duelling book. But the powerlevel of the decks would be an issue, i cant let an lvl 1 player char play full power dragon rulers, so each player should play a weak deck with a limited amount of key cards (satellarknights with only 1 deneb or shaddoll with only 1 shaddoll fusion), you can of course later upgrade your deck with better card or even change your decktheme. Boss npc would be playing the strongest decks in yugiohs history, with disregard of the banlist and have the use of duellinks like abilitys. We will be playing prelink era, so most deck arnt completly useless. The setting would either be gx-style duelling school or a mix between 5ds and duelling monsters. Im also going to hide summoning methods behind a lvl barrier, i dont mean "until you are lvl 5 you cant synchro summon", more like you cant use synchro monsters that use synchro monsters as material until certain lvls or summon during your opponents turn etc, anime style. If you have questions simply ask, right now its just a brain child.
