During that time they were certainly a masterpiece factory. From 1995 with their first film Toy Story, to 2004 with the release of The Incredibles, that resulted in consistently great films for 9 years. Their record held for 11 years until Cars was released in 2006.
I believe no other studio has had similar performance. I remember around early 2000's news of Hollywood studios in panic because investors started asking other studios why it was considered business as usual, a given, that for every successful film a studio released there would be flops too. So like VC investing, the pay off for the eventual success had to be enough to offset those films that flopped and lost money.
But then came Pixar and suddenly a studio proved you didn't have to have flops, every film they made in their first decade was a resounding success. They blew the conventional logic of Hollywood economics out of the window.
This article sort of paints a picture of how outstanding their success was at the time: https://www.theguardian.com/film/2004/nov/12/3
So I guess I disagree with the title, Pixar was most certainly a masterpiece factory in its first decade.
Reading deBoer's article I can't say I agree or disagree about the recent state of Pixar, I grew up with Pixar films and their first decade coincided with my childhood and early teenage years, so when I think to myself "yeah Pixar's recent work doesn't touch that early magic" I can't really tell is that my bias coming through?
Maybe I am overthinking this a bit.