I agree with this in almost every regard. I really don't like the drift towards sandboxed apps where HTML will do just as (or more) nicely.
But: money.
Solve subscriptions. This is what the apps do. Adobe DPS, which I mention below, is so totally geared to creating paid subscription content.
The Readability fiasco was unfortunate since I'd like to see other non-ad based approaches to paying open content publishers/creators. Unfortunately, no one on the vested interest side of the fence (including Apple) has any real motivation to solve for this.