Wind Waker used to be my favorite, but after a recent playthrough of it (a couple of months ago), I've found a bunch of nagging issues I have with it.
Perhaps it's just that my tastes as a gamer have changed since I last played it, or maybe it's the fact that Skyward Sword recently wowed the everloving hell out of me (the two may or may not be related), but I find that I don't enjoy sailing as much as I thought I did. It takes far too long to get from place to place, especially if that place isn't in a cardinal direction and right next to the island you're leaving from. Change the wind, wind-changing cutscene, sail for 5-7 minutes to your destination, whoops slightly overshot the island gotta turn around and sail slooooooooowly towards the coast and/or majorly overshot the island gotta turn around and change the wind, wind-changing cutscene, etc.
It's quite tedious, especially in the first half of the game when you don't have access to the Ballad of Gales. Furthermore, I used to give the Great Ocean a lot of props for having a lot of content/islands to explore, but...what kind of crack was I smoking back then? A good third of those islands are nothing but mini-gauntlets, most of them with the same layout (3-5 doors with a medium-sized central area and various enemies to kill inside each door) and meh rewards (yay, a rupee that I can't fit in my largest wallet anymore because this game throws money at me like a drunken dad throws his redheaded stepson at the wooden door). It's fine the first few times, but gets boring to me pretty quickly. Another good third of them are nothing but housing areas for treasure chart...erm, treasures. Not really the type of thing I find very entertaining. I like games with lots of content, but when a bunch of that content is doing the same thing over and over, it tends to grate on me. There's a reason I've never 100%ed Wind Waker like I've planned to in the past, and that's the main reason why.
I find the pacing generally awful as well. I judge each Zelda game by the time it takes to get to the first traditional dungeon. I don't really count Forsaken Fortress, as it's basically a glorified stealth mission until the very end when you finally get your sword back to kill a whopping one enemy and get tossed across the ocean. So, that's Outset, Forsaken Fortress, text dump, Windfall, saaaaailing, doing a bunch of menial tasks for the Rito, THEN the first dungeon. I've played Wind Waker dozens of times, and yet that whole sequence of events still takes me a good, what, 2-2.5 hours to get through? That's way too long to get to what I consider to be the meat of the game, and unlike Twilight Princess, I didn't even find most of the stuff until then to be particularly interesting.
Still speaking of the pacing, the goddamn Triforce Quest, oh Geebus. To be fair, searching for the Triforce Charts was quite fun. Especially the Ghost Ship + resort ones. Looooved those two. What killed me was searching for the actual shards. Those damn light beams barely helped me, considering they disappear while I'm still too far away from the treasure for me to get an exact bead on where it is and what follows basically amounts to a pixel hunt. A lot of times, I end up uncovering an Octorok instead, meaning I have to fight it off and by then, I've lost my bearings, meaning I have to back waaay up so that the light beam shows up again to repeat the process and arglebarglebargle. Also, having to deal with Tingle in any context is arglebarglebarglebarglebarglebargle. God, he creeps me the hell out. >_>
Another problem I had is the dungeons. For me, I consider the dungeons to be the meat of the Zelda series, the very reason I play the games. I was quite disappointed by the majority of them. Not until The Tower of the Gods did I think they started to pick up, and even then, I only got a lot of enjoyment out of that, and the two Sage temples. The partner mechanic for those two was admittedly interesting, but I think that they hurt my experience with the temples more than they helped. I didn't particularly like using a song to switch between characters every time I needed one of them to solve a puzzle. Found it quite tedious, really. Medli was mostly fine control-wise, but controlling Makar's flying through the Wind Temple's confusing central room kinda ticked me off. Thankfully, I enjoyed both dungeons' layouts and puzzles well enough, and that was enough for me to come out of them with (mostly) positive feelings afterwards. The final dungeon disappointed me, too. I'm not at all a fan of the "reuse layouts/themes for every dungeon up until now" thing. Screams "lazy" to me, you know? Although the final battle was pretty kickass, I'll readily admit.
Wasn't very impressed with the music, either. This might be blasphemy to say, but (until Skyward Sword) I've never been much of a fan of Zelda music. Focuses a tad too much on ambiance/mood-setting for my liking, especially for dungeons. I tend to find the concert/live-performances far more interesting than the actual in-game music. While this was less true for Wind Waker, what really made me dislike its music was the sound quality. Oh god, that synth quality, ugh. Not nearly as bad as Twilight Princess', but it's definitely up there for me. Music is a huuuuge part of gaming for me, and my disappointment with WW's was a big strike against it.
Adding to those are my mostly minor issues with it. Flat facial textures, Tetra being relegated to little miss rescue me at the halfway point, etc. It may sound like I hate the game, but I really don't! I still love like it! The art style is fantastic (if a bit loud), the characters are full of personality, it has the best version of Ganondorf, some of the best enemies in the series (F*ck yeah, Darknuts!)... I just love it a looooot less than I used to. :|