I disagree. If it's not worth backing up (locally), it doesn't deserve protected status on the phone.
Or to put it another way, if it's important enough to retain when storage space is low, it's important enough to retain for when you have to recover from a backup.
I think that is a decision best left to the developer or user. Take an app that syncs your photos from a site you may already use, like Picasa, Flickr or SmugMug. You want to have these available on your iPad or iPhone instantly, even when you are without internet service. But you don't need them backed up to your computer every time you sync, causing the backup times to skyrocket, and if you lose them on a restore, it's a minor inconvenience, but not a huge deal. Losing them unexpectedly when you don't have the time or ability to re-downlaod them is a much more major problem for some people.
You left out the case of storing data for offline use, which is one of the key use of Instapaper, offline maps, cached notebooks, etc.
If I stored something specifically for offline use, I want it to be available as long as my device is with me, even when I'm offline. (1) Some of it is important as you say, and they should be backed-up, but (2) some are important, but is capable of being downloaded again and shouldn't be backed up and shouldn't'. The latter is the one that is now automatically cleaned up.
