It's quite hard to make a game story as compelling as Planescape. But I love both games dearly so its okay. I don't think a story arc between the main character and a companion has ever surpassed Dak'Kon and TNO. That revelation stuns me to this day.
IMHO nothing in my mind even comes close to Planescape. Usually when I rate my top 10 RPG's of all time, I need to do it in the context of the era it was released. For instance I would put Dungeon Master and Wizardry VI in my top ten of all time, but if I played Wizardry today as say a new release, it would obviously be underwhelming. Planescape could be a new release just today in its original form, and I'd still put it as #1 purely by virtue of its story, brilliant puzzles, and unique world. It's just that fucking good.
I still remember seeing the box at the store and almost not buying it. It had received almost no hype or marketing, the box art was blah, and I didn't know what "Planescape" was, I wanted forgotten realms or whatever. But it was D&D, didn't see anything else that caught my eye, and honestly thought I was setting myself up for some generic experience. About five hours or so later, I basically realized this was pure gaming heroin with a finite supply, and I needed to make it last and enjoy every moment of it. Probably the only game I forced limited myself in playtime to extend out the experience as long as possible, because I didn't want it to end.
Everything about it was brilliant. The character interactions that evolved each NPC's story, Dak'Kon's sword lore, fall from grace-- everything and anything that had to do with story was Epic Tier fantasy writing. There were multiple times where I just sat there gawking at the brilliance of the story-- the Dak'Kon story arc you mention, the reveal with Morte at the tower of skulls-- just fucking brilliant. Throw in the brilliant puzzles with multiple solutions, the tattoos, and the brilliant lore around every single weapon/item in the game, and it's just perfection. Probably the only game where I cried at the end with its amazing finale, staring at the screen unable to accept it was over..
So yeah, I'm a pretty big Planescape fan. Was crushed that the "sequel" sucked so bad.