I wouldn't call PB's games philosophically deep, but to claim they were inconsistent and made it up as they went along is just foolish. Story-wise, I can't think of an open-world aRPG that's better save for perhaps Divinity II.
*SPOILERS*
In the end sequence of Gothic 1, the Nameless Hero (NH) emerges from the Temple of the Sleeper, into daylight, and observes that the magical barrier has fallen. Then in the intro to Gothic 2, the NH retroactively lies buried beneath rubble in the chamber of the Sleeper, is teleported out by Xardas, and is clueless to what has transpired.
The orcs are suddenly redesigned in Gothic 3; their appearance, their intellect, and their culture, is significantly different from what it was in Gothic 1 & 2.
If I recall correctly there's one thing Xardas, Vatras, Pyrokar, Lord Hagen, and the quest journal, all agree on: The Eye of Innos can only be wielded by the Chosen of Innos. The idea that the Nameless Hero is the Chosen of Innos is consistent with Gothic 1 and 2, but then during the development of Night of the Raven, PB apparently changed their minds and decided that NH should be the Chosen of Adanos instead (the game strongly hints at it in the final confrontation with Raven, and Mike Hoge has confirmed it 100% in an interview). If they had planned that NH should be the Chosen of Adanos, they wouldn't have introduced all the material about how the Eye was exclusive to the Chosen of Innos.
How did Gorn know where the first rebel camp (Reddock) in Myrtana was located? He had just arrived, and he didn't have contact with the mainland during Gothic 1 & 2 (Reddock probably didn't exist during G1+2 either). Yet he immediately leads us directly to it, between the two nearby orc patrols that are searching for it…
Then of course there's the interview with Sascha Henrichs (http://www.worldofgames.ro/sascha-henrichs-interview/) where he says that the pyramid in Khorinis was completely random at the time, because they didn't know what to do with the game area. He goes on to say that "the new world itself also consisted of a few different land masses that were happily patched and thrown together without an idea of a design. There was just this Pyramid and based on this, we created the NOTR world. The desert canyon was actually a prototype for another project we worked on, just after Gothic 1. But it was never finished and to not discard all the effort we put into this, I decided to weld this canyon into the new world. It was a “stunt” but somehow it worked in the end haha."
These are some of the reasons why I think PB made up things as they went along, and why I think that they've been rather inconsistent.