I prefer the MTG way. Yu-Gi-Oh has that as well. With YGO though, you have a game board, and can only play with the cards you have already set on the board (unless a card effect says otherwise) You have creature/unit zones (up to 5), as well as trap/spell zones (up to 5). You then have an field spell zone (only 1 at a time) which changes the environment of the whole game, and then your deck and grave yard zone. That will help with limiting combos, and complete player dominance which is different then MTG, where there is no limit. With YGO you can use a trap any time, yours or your opponents turn. However, with spells you can only use them on your turn, unless they are an instant. Spells are used to beef up yourself or your units, and traps are usually used to counter your opponent or tear down their units.
I am not saying we should limit the amount of cards one can play. I think if we take the good things from both very popular card games, we could have really good mechanics with our game. To answer your question: It should be turn based. With every action there is a moment for reaction. For everything I do, you have a moment, even if it is ever so brief, to choose to counter what I did. A simple button to skip the counter moment, or you have a card you want to click on that is a trap that kills off the unit I just laid, then you activate it, my unit dies, and I continue with my turn. If you declare the attack phase, I have a moment to stop it, or not if I don't have the cards or choose not to play them. Hope this gets the hamster running a little.