Adding numbers to cards to signify the ordering would be really beneficial.
For example, when activating Kashtira Ogre’s effect to excavate up to 5 of the opponent’s deck and multiple copies of the same card are revealed. You do not know which one would be their top deck or the order of the rest of the cards. A system like this does exist in EDOpro, for example.
Additionally, when the cards are revealed, the pop-up box does not show the excavated cards in the same order as was revealed from the deck.