Thanks for the reply. Good points, but for people with new devices that's not very pertinent. I still think it should be a configurable option. There are MANY situations where people simply don't need to store a local copy of apps on their computers just to be permitted to sync music/books/photos, etc. As it is, I think most people (with modern iPads) do ALL their app updates on the device itself (at least in my experience - in seeing hundreds of iPads belonging to clients, friends and family members).
That said, I do have an old iPad 1st gen floating around the house -- so I saved a copy of all my apps on my server around the time iOS 5 came out - for that very reason. Wouldn't it be nice if iOS was updated using progressive enhancements, so that older devices could be updated, but without the features/apps it's processor/ram is unable to handle. This way at least the libraries/frameworks would be updated enough to run modern apps (where possible, given the processor/ram restrictions).
As a side note, Apple really should keep the most recent version of an app that's compatible with older versions of iOS. For all the people stuck on iOS 4 or 5 with older devices, it's a shame Apple can't retain a single copy for download for these people. In the grand scheme of things we're not talking about that storage/time/money.
Funny you mention deleting them... because that's what I do for people in low storage situations (delete the apps that get transferred. However they re-transfer on every sync, so I'll make symlinks or empty files with no write permission with the same names as the files. This causes iTunes to throw an error, but it ultimately fails to write the file (which saves space). Unfortunately this is NOT a solution you can give to normal people, as it throws an error AND when a new version of the app comes out (with a different filename) it will have no problem downloading it.
On my personal computers I use an app called "Hazel" for automated filesystem cleaning - it can watch folders and take actions when new items arrive. It's like Folder Actions in Finder, but it has a full workflow UI. Think of it as a simplified Automator for taking action on files. It's great for this problem: On my personal laptop I have it set to delete all apps from the Mobile Apps folder (and a number of other places) on a regular basis to save space. This could certainly be done with Automator, but I like Hazel's interface and simplicity. I have the largest (768GB) drive for my MBP15r (with no third party storage upgrades that are larger), so I'd like to keep the disk as low as possible for as long as possible. Hazel helps me do that, and keep my downloads folder reasonably clean.
Sorry for all the tangential thoughts...
Cheers,
Jackson