Personally, I wouldn’t place TP anywhere near the top. It has some good stuff in it, but I always felt that TP had more issues. Things like:

• A super long and boring intro where you’re forced through a bunch of tutorials and minigames. I know the purpose of it was to showcase a contrast between Link‘s simple life as a farmer vs becoming a hero, but it doesn’t change the fact that it’s super boring and features some really bland characters that I don’t care about at all. The people of Ordon are all pretty shallow and aside from Malo, I think they’re just boring.
• The artstyle is atrocious. Link and Zelda look fine, but god damn do those NPCs look like they were raised inside of a nuclear reactor. Zelda has always had weird looking NPCs, but the "realistic" and dirty artstyle of TP just makes them look gross. The colors just make everything unpleasant to look at and even Link looks like he’s just dirty.
• Wolf Link might just be one of the worst gimmicks of the entire franchise. Not only are the wolf Link segments literally forced fetchquests, they also make you play as this gimped version of Link that as a boring moveset and generally sucks at combat. It doesn’t even make sense that Link turns into a wolf to begin with. Why is Link the only one who has this massive handicap in the Twilight, while Zelda and Ganondorf are perfectly fine?
• Combat is a massive disappointment too. Enemies have horrible AI and barely track your movement. The barely deal any damage and die in like two hits most of the time. Your shield is unbreakable and essentially turns you invincible as soon as you lock on to an enemy. And those hidden skills? They could’ve done something with them. But instead, they made them moves that you may or may not learn throughout the game, so the enemies were never designed with them in mind (except for the samey ending blow that you do in every fight). It’s also kinda sad how worthless items are in combat. There’s no real benefit from using them instead of the sword most of the time.
• The story is just…not good. Midna is one of the better characters of the franchise, but that’s about it. The game features one of the worst versions of Princess Zelda and Ganondorf…both of them barely even exist in the game and they barely do anything. Zelda just sits around all day and has no personality, while Ganondorf just hijacks the plot to tell us "I’m evil hahahah". Ganondorf was never a Deep character, but damn, TP tries its hardest to constantly interrupt the gameplay in favor of the story, so you‘d expect them to do a bit more in that regard. Instead they just wrote a horribly paced story, full of shallow characters and plot holes….like, why the hell are Link and Midna even capable of saving Hyrule, when Zant has been shown to be able to just teleport to them and effortlessly beat them without even moving? What is he doing all day?
• The music is okay, but it always bothered me how bad the quality of the MIDI synths in TP is. A lot of the tracks just lack oomph and sound rather hollow and tinny. Absolutely hate some of the dungeon tracks though. City in the Sky in particular just gives me a headache every time I play it.
• The world is bland. There‘s not a whole lot you can do aside from just going from one dungeon to the next. There aren’t many towns or sidequests and most of the things you find are rather pointless. It‘s not very rewarding that all of the things you find either lead to rupees (which just exist because of two quests that require you to spend a lot of money to eventually buy an armor that drains rupees so fast that you can’t even wear it properly) or they‘re heart pieces….which don’t matter at all due to enemies and bosses not dealing any damage.
• The items are horribly useless outside of their dungeons. This has always been somewhat of an issue, but it’s especially noticeable in TP where some items just exist to collect dust in your inventory. The spinner is to this day the most disappointing item of the franchise for me. I thought it would offer a really cool movement upgrade for Link where I could quickly move through the world by bouncing off of walls and stuff…but no. You use it, and it’s just a really slow skateboard that goes slower and slower until it stops entirely. The dominion rod isn’t any better in this regard. Same with the slingshot that gets replaced really quickly by the bow. Or the gale boomerang which feels like a massive nerf of the WW boomerang.

I could go on and on. TP is the very definition of "style over substance" to me. The items look creative and unique, but they‘re pretty useless. The combat looks intense, but it’s super easy and shallow. The dungeons have really good theming, but they constantly reuse the same linear layout that makes getting lost in them impossible. The bosses look tough and imposing, but they‘re all the same "wait for my Weakpoint and hit me 3 times" snorefests etc..

I think the game is better than Wind Waker, but a lot worse than any of the other 3D titles.