It annoys me when they take the card before I have finished my meal. We found all the new ones at DTD the worst, their excuse was its a 2 tier process, unlike the Disney owned restaurants where they just do one transaction at the end of the meal. The others apparantly take longer to process and prefer to start it before the meal ends to save the diner hanging around.
Personally I don't care what the process is like. I don't want hassling with it til the end. I slightly lost it with our waiter at T-Rex, we had only ordered our drinks & entrees when he asked for the cards, I told him he would have to wait until the end of the meal, I told him he had no idea what desserts we wanted or if I was going to ask for his 18% tip being removed for poor service. Thankfully the service was good after that, he took the card at the end, he got his 18% and everyone was happy so why annoy people?