I think Water, Shadow, and Spirit temple were my favorite since they offered the most variety for me. Other than that, the puzzles were rather simple. I guess Forest was fun just for the difficulty spike after becoming Adult Link.
The Forest and Spirit Temple is pretty cool. The rest of Adult Link's dungeons are not bad, but they don't do much for me. I really dislike Young Link's dungeons though, I find them so boring that they make for the worst first half of any Zelda game imo.
It also doesn't help that the combat feels wrong to me in OoT. Whatever it is about it makes me want to avoid every fight just like in a 2D Zelda, which is unfortunate.
Out of WW, TP, and SS, I usually hear TP getting the most praise. WW is getting praise again, but I think it's to the same effect as Majora's Mask where people give it a chance over time. Overworld being empty is one of the flaws from OoT that pretty much carries over in every 3D Zelda for me. While TP's one of my least favorite Zelda's, I'd say it had some of the better dungeons of the 3D ones.
What bogs it down for me are the graphics, art style, slow beginning/pacing, item usage after dungeons, and wolf portions.
Definitely not a bad game, but not one I'm eager to go back to. I'm more of a 2D Zelda fan though.
I feel like I never see TP getting much praise, but I guess I only ever see the vocal minority. :/
I do personally think of it as a better game than OoT though. It has without a doubt some of the best dungeons in any Zelda game. While I agree that the graphics and art style are not great, I feel the game makes up for it when it comes to the design of everything, especially the dungeons, I think all of them are interesting visually.
The slow beginning is really unfortunate, those early game wolf sections really drag. I actually like the wolf though, sure it doesn't add much overall, but it does give us the best way to move fast in any Zelda game, that alone is enough of a justification for it's existence.
I also agree that the item usage after dungeons is really bad. Though at least we are still able to use them(OoT boomerang why?), nor are they a bunch of upgrades to items you already have. It's still bad design.
I like TP's overworld. Yeah, it's pretty empty, but I also like SotC's overworld. I guess I'm a sucker for massive overworlds.
It is certainly a flawed game, and it's not my favorite Zelda or anything, but I would return to it much sooner than I would OoT.
I'm also more of a 3D Zelda fan.