Like others, i agree that it depends on the game. Zelda is about adventure and exploring so it would be quite annoying to be stopped every 5 seconds and wait for the battle screen to come up and fight a moster by taking turns or waiting for a time-counter to go down then watching a little "yey i won" scene then seeing what items you got, with the whole process taking 5 min or more. The fun about games like final fantasy is building up your character to see what new spells or abilities they have...so yea, even though that whole battle process takes a while, its exciting to see how much experience you have and how close you are to the next level and so on.
However, when it comes to turn-based or ATB, I prefer turn-based because you only have to wait for your enemy to make their attack in turn-based games while in ATB you have to wait for the counter to drain......boring.