So, TP is better than SS?
I think in the end I'll prefer TP over SS, yeah. I like Wind Waker more than both, I think it's tied with Link to the Past as my favorite Zelda.
It's kinda hard for me to say as both games had their flaws. SS was more of a proving ground for a new type of control style that I liked even if it wasn't perfect but it suffered from a great number of smaller flaws that almost robbed the Experience from the Zelda Experience; whereas TP tried to do something new and potentially interesting with the plot only to drop the ball and turn itself into a updated OoT clone, like promising us a new villain in Zant who quickly devolved into a goofy Aganhmin wannabe along with all the other dropped plot threads. Where TP's world felt dead and barren, SS's world felt undeveloped and bottled up.
As for inventories I felt that SS definitely had the advantage due to being more streamlined and less "Here's a fun dungeon item. Let's make it completely unusable outside of the dungeon until you run a sidequest to repair it so that you can move a handful of statues and then leave it with all of the other fun but almost impractically useless items.". Though I will admit that SS's sword upgrade curve was ridiculously uneven and bizarre, but even then it still beats out never gonna get any stronger wolf form, plus you could appreciate it more thanks to SS's boss rush and Hero Mode's Skyward Strike carryover. Plus those Medals passing on passives was a good idea but was underutilized (kinda like the Oracle's ring system but with stackable effects instead of only one at a time).
And then there's the challenge which I felt could be split fairly evenly. TP's fights had teeth on them and the challenge cave actually made me use stuff I wouldn't normally use which was a vast improvement over the games that had been coming out prior (although part of the challenge cave's challenge was remembering just how nerfed potions were in this game) but where it really shines was in boss combat. Many boss fights felt fun even if they slavishly adhered to the rule of threes and gave us some memorable ones like well pretty much everybody but the water dungeon's boss. That said I felt SS's scrub fights were better for the most part even if it lacked variety at times. The boss fights on the other hand were on average inferior to TP's boss battles with a couple of exceptions; namely level four's boss, level five's boss (kinda), the third fight against Grighamn, and the final boss fight.
Additionally SS's dungeons were both weaker and fewer in number than TP's but they were also shorter in a more realistic sense versus TP's level 1's wind valley and level 4's how do anybody get into this Colosseum? Though TP did have levels 5 and 6 for its more realistically proportioned dungeons. Though part of this was the fact that most dungeons had to fully showcase their respective items before letting them rust in your inventory for the rest of the game whereas SS had you running around and using shit all over the place to get anywhere.
I believe both games have about the same signal to noise ratio of NPCs in them but SS simply had less of both. It basically comes down to Minda, Malo, and the gang versus Groose, his gang, and Scraper. Though SS's Zelda at least had the decency to actually come out and say that Link was her tool before making her worthless non-sacrifice versus TP's Zelda dropping vague hints to things that'll never come to pass before making her not as worthless until it becomes even more worthless non-sacrifice (she had me going the first time around since the series hadn't pulled something like that before; now I just laugh). Ultimately though TP's Zelda wins simply by virtue of being a boss fight
even if she has a void where her nether region is supposed to be
Additionally both had their stupid realms. TP's Twilight Realm and its glowy bug hunt versus SS's Silent Realm and its glowy drop hunt.
Tl;dr: would be that I'd give points to SS for having a better overall plot, a better inventory, better scrub fights, and better non-dungeon environments and I'd give points to TP for having better enemy variety, better dungeons, a better selection of bosses, a better Zelda, and better overall music. Overall I'd rate them the same since despite TP having more items scoring points under its belt that inventory matter is something I'd dock it for.
(The tl;dr of my tl;dr is that if you like aesthetics TP's the better game. If you like mechanics then SS's the better game. It really comes down to preference on this one.)