FWIW, I agree with you that this is a major step backwards. Then again,
the internet and iTunes Store never, ever, ever go down or are unavailable!!
The "new improved way" to make sure your iTunes library has the same app
versions as your device:
1. Open iTunes.
2. Select the Apps pane.
3. Select Updates.
4. Download the updates to iTunes.
5. Connect your device to your computer.
6. Wait for backup and download of Apps to the iPhone to complete.
The alternative "improved method" is to download app update/purchases to the iDevice
and also open iTunes and do the update within it as well (Download app twice!!).
Isn't this sooooo much easier than simply download to the iDevice and then
have the apps backup to iTunes when syncing!!!!!
There is a whole lot of doublespeak about "app trimming" requiring the change, which
in reality is just an excuse for not writing an application for how people really use it.
After all, Apple knows which devices you have, can't iTunes be written to be smart enough
to deal with it!!!!