> Aggregated analytics do,
Good.
> and you can't run a serious website without some kind of analytics.
I don't believe you.
> Preference-storing does as well, despite any reasonable user expecting that, if they set a preference, it will be saved.
IANAL, but I'm given to understand that this is untrue.
You're right about explicitly set preferences.
What do you see as the harm in website owners using aggregated analytics data to improve their sites?
Abstract: It's still spying on users.
Practical: Supposedly-aggregated stats have a history of actually being perfectly possible to analyze back into individually identifiable information. Also, it's conveniently the same tech stack in a way that makes it easier to make an actual slippery slope.