ExploderWizard
Hero
I like your points. I think they make nearly any published adventure hard to run as published. Almost all published adventures either set out an area and its inhabitants, or set out a series of events/locations for the PCs to progress through.
With the former, it is very hard for "what happens next to make sense in the context of PCs, NPCs and setting" unless the GM injects most of that content. Or unless you count as "makes sense" nothing more elaborate than the orcs from room 2 rush in when they hear combat between the PCs and the orcs in room 1. That is a very narrow form of "meaningful choice" which is well-suited for a certain sort of classic D&D game but I think is different from what many contemporary players are after.
With the latter - event/travel-to-locations type adventures - the basic issue is that the story of the PCs is prescripted. Which is mostly at odds with "reactions/outcomes to previous activities demonstrating an effect and change on the setting".
A good example of a module with a plot, that does not also pre-script the story of the PCs is L2 The Assassin's Knot. The module is a murder mystery investigation that leaves players to their own devices on going about solving the case. There are location & NPC details, and also a timeline of events which will progress in a certain manner if the PCs do nothing or are ineffective in their efforts.
It is available free on the wizards website
http://www.wizards.com/dnd/article.asp?x=dnd/dx20001229b