I would argue that the issue with The Colour of Magic and The Light Fantastic isn't that they are bad. It's that they are more visibly parodies of the fantasy genre. Cohen the Barbarian is a clear parody of Conan, complete with snake cultist temples and the like. The Wyrmberg is a direct parody of Anne McCaffery's Dragonriders of Pern. Early Ankh-Morpork references Lankhmar. Vance's Dying Earth magic system is directly parodied in The Light Fantastic. And so on.
The fifth novel, Sourcery, is where things started to shift from parody to world-building. The plot fundamentally changes the way magic works, allowing the wizards at Unseen University to settle down into their dysfunctional roles without having to worry about assassinations and the like. It also brings Vetinari more to the fore as the Patrician.
And while I think that Thud! is Pratchett's greatest work, I have no idea what someone reading it as their first Discworld novel would think of it. I went into it having read every preceding Discworld novel and was fully aware of Vimes' journey up to that point. I'm sure that helped me appreciate the novel in all its wondrous, chaotic glory.
I was disappointed with Vimes' last novel, Snuff. I felt like he'd become a real Gary Sue. Part of the appeal of Vimes is that, despite always being a step behind the villain, he doggedly hangs on and finds a way to win. In Snuff, it felt like he was always one step ahead of the bad guy, so there was no real tension.
Same with Raising Steam. The deep dwarves were rather pitiful compared to the credible threat they'd been in Thud!, and having Vetinari moonlight as a steam train stoker was just plain silly.
I also disliked Unseen Academicals because it felt poorly written. It's been a long time since I read it, but I think it must have been the one he was working on when he was first diagnosed with Alzheimer's and perhaps didn't have the support he had with his later novels.
And then The Shepherd's Crown ... what a limp way to end the series. I'm sure Pratchett's Alzheimer's was really bad by that point, and I'm sure he just wanted to tie everything up in a nice little bow, but after reading this one, I wished he hadn't written it. I feel like it does a disservice to both Granny Weatherwax and the Elf Queen.