The main difference between the two that immediately springs to mind is that YGO has trap cards which can be used during the opponent's turn. Whereas in Pokemon only under very rare circumstances can the opposing player interfere with the turn player's turn. In Pokemon, you can place your Pokemon on the bench freely, whereas in YGO there is a limit of only one normal summon per turn (though you can special summon as often as you want, so it's not that different I guess). Winning conditions are different between the two games as well. You will lose in Pokemon if you can't put an active Pokemon out but in YGO, you are free to have no monsters on the field at any given time.
A competitive difference between the two is that in Pokemon, drawing a large amount of cards in a single turn is fairly standard but in YGO, draw power is far more advantageous. This is because YGO has a ban list that limits the amount of copies of certain cards but this isn't the case in Pokemon. Often drawing into those power house cards in YGO gives the player a decisive advantage, which makes draw power in YGO so powerful.