Like many games, where PS:T shines is in the little things. The main plot does indeed have a weak third act and though I quite liked the finale, it's nothing mind blowing. However some of the smaller moments leading up to that finale are fantastic and what, in my mind at least, are what elevates PS:T above most other rpg.
You kind of dismiss it in your argument, but take for example how PS:T handles world building. As an example of that the 'Brothel for Slaking Intellectual Lusts' is a relatively minor part of the game where you'll encounter and probably recruit Fall-from-Grace and in most games wouldn't be very memorable, but in PS:T it's full of dialogue and interesting characters. Side-quests, skill checks, and a slew of entertaining personality. It's a full fledged location with an interesting story all of its own, and only one of many such locations in the game.
I also really like how player progression is tied into this world-building as well. You don't just get to pick a class but have to interact with characters within the world in order to learn it through associated quest and dialogue. It helps make both the world itself as well as the Nameless One a bit more alive.
Then we've got the characters themselves. Annah, Fall-from-Grace, Morte, Dak'kon, Ignus, Nordom and Vhailor. Your interactions with them are fantastic with great little moments like studying the Circle of Zerthimon and learning about your previous incarnations interactions with him. It's also interesting that you might not even encounter some of the potential companions or that they have the potential to turn against you depending on your interactions with them. I like when games give companions a bit of incentive of their own. Not just the party members either but also side characters like the tragic Deionarra or even the Nameless One's own previous incarnations, people you might or might not learn about given how you choose to play the game.
Another element of the writing I very much enjoy is just the sheer volume of details that can easily be overlooked or missed. The game is full to the brim with secrets, especially in the early part of the game as you explore Sigil. I've played through the game twice yet still know there's tons of stuff I've missed, and although some don't like that and prefer to be capable of getting 100% completion every playthrough, I'm not one of those people.
Which all isn't to say Planescape: Torment perfect by any stretch, even writing wise. In terms of gameplay PS:T is pretty poor with basically non-existent balancing and muddy visuals making combat into a confusing jumbled mess. Writing wise the game can sometimes get way too long-winded and not all the dialogue feels fluid or realistic, but then given the weird setting and sorts of characters you're interacting with I feel that it can be forgiven.
Also it's old and reflects a lot of the drawbacks of the time.