Pfft. You could argue that both Thiefs had worse and worse mission design the further you got.
And you still would not be right, since both late games have so many bright spots as well. Just like in Thief 2 Casing the Joint and Soulforge were horrible, but Life of the Party the best mission ever, both Undercover and Return to the Haunted Cathedral are awesome while Strange Bedfellows and The Maw were less than stellar in Thief 1. Much less. Usually when it comes to arguing over Thiefs, there's the people who hate supernatural stuff and the ones who can't help but love it.
Often people prefer one game over the other based on which one they played first, but since I don't know which one it was for you, I'll go on a limb and say that you played the second one through and never finished the first. Otherwise you wouldn't bother with lies like "better mission design" or "better story". Seriously, you thought the whole rust gas business with Karras made a compelling plot? Heck, I was just following the thing because the missions kept being decent. Truding deep into the City's pagan plots was far more interesting, especially since Garrett actually had a reason for following the plot besides the archaic "let's save the world". I'll grant that the narrative was better in Thief 2, in Dark Project it took longer to get the plot going and any hooks in place(Assassins) and ther weren't many ties to the main plot arch until The Sword/i], while Thief 2 started throwing them to you after Shoalsgate Station and didn't let go.
Maybe you just don't like the supernatural elements there. Too bad.