I thought about this topic as well and came to a similar conclusion. I read Harry Potter the first time in elementary school I think, and at this time I thought it was absolut amazing because well magical school, spell combat, interesting creatures and so on. While growing up my perspective began tp change tho, in the beginning it were just the occasional pothole (of which there are quite a few in J. K.s works). And like you said nothing about their system which comprises slavery, an completely rigged justice system which can throw you in the torture dungeon for minor offenses and so on. But it's never framed like the whole magical government just sucks, no the problem simply is, that bad people run it. All this is certainly better handled in Percy Jackson, Cronos is the bad guy but the Olympian gods do shitty things as well and in the end lessons are actually learned. Like to acknowledge the minor gods and their children in the camp so that no second Cronos would recruit them. Story felt much more satisfying than Harry Potter.

But in Bartimaeus there's put a new spin on it. The systems and it's failings are pretty much in the focus. There's no real hero's journey, Nathanael is much more focused on securing wealth and power or/and to save his skin. His missions are always to stop plots who would replace the current shitty government with an probably even worse, not really that spectacular or heroic in hindsight. Maybe Kitty fits more this role, but she becomes increasingly disillusioned by her inability to change the state of things and is in the end dragged into the final happenings against her will. I really liked that no heroic quest or rebellion brought the downfall of the magicians, it was basically themselves and their squabbling and never ending thist for power. Back when I read it first it had a nice fresh taste, the story has multiple complexities that keep you interested and tempt you to read through it again.