The apps themselves are usually not "inferior experience". They can be snappier and better offline performance. That's not to say I disagree with all of the other things you said.
My experience is counter to this - most apps created from websites are inferior experiences.
Most common reoccurring problem I find is that all links off-site, are displayed in a webframe. Which doesn't give me access to the normal things that Safari does - I can't email the page, add it to my reading list, or bookmark it, so inevitably I always open it in safari. I'd've rather stayed there in the first place...
But this is not the only sin, just the one that leaps to mind.
