(I’ll just repeat that I found MR more enjoyable the second time around, the first time I think I felt the same way as you do, it was certainly my least favourite Discworld book).
I’m still, not convinced that the earlier books had more complex villains or morals. Small Gods for example has the moral ‘organised religion is bad’ (or possibly ‘imposing you religion on others is bad’), and riffs off that all the way through. Vorbis is not a complicated villain, he just wants to keep invading countries because that’s what Omnia has always done. In the Death books The Auditors are almost literally two dimensional.
In fact your example of Vetinari is a good one, in the early books he’s just the tyrant of the city, but as the books go on he’s humanised to the point where he becomes a sympathetic character.
Admittedly I’m having trouble coming up with a more complicated villain from the later books, Reacher Gilt and the Lavishes are just pretty straight forwardly Bad People.
As I said I’ve been reading through all the Discworld books, and now I’ve only got Snuff and Raising Steam to go. So by this time next week I’ll probably never have another new Discworld book to read. That thought has actually been bringing tears to my eyes recently. Fuck Alzheimer’s.