TWW did a lot of things very well, but it also had its incredibly infuriating bits. It comes out ahead of PH if you just run this sort of checklist, but, in my opinion, two elements of TWW end up bringing it down quite a bit.
PH has its repeating dungeon, and I'm not happy about that, but you do that only three or four times and it takes no more than fifteen minutes each time (usually less). Plus, it's only about seven or eight minutes of each run that you're redoing parts you've already seen - there's nothing wrong with any part of that temple when you're seeing it for the first time.
TWW, first and foremost, has some absolutely interminable sailing. You're looking at about a minute of travel time between two adjacent islands, and there are times when you have to go from one end of the map to the other. Even after you get faster transportation, you're still looking at about a minute or two of travel to get most places.
TWW also has a horrible fetch quest. First you have to find nine (!) items, most of which require little more than a quick puzzle or a fight with a roomful of basic enemies but all of which require you to travel to the ends of the earth. Then you have to take all nine items elsewhere and pay exorbitant amounts of money to make them useful (this sometimes requires that you also spend some time treasure hunting). Then you have to go to nine more different sectors in order to listen for music and to tap a button. It takes forever and it's one of the most unrewarding experiences I've ever seen in a game.
PH is a better game than TWW for the simple reason that it doesn't make the player spend something like two or three hours wishing he could get to the next part of the game.