How can I stop iTunes adding apps I've deleted onto my phone?

I have an iPhone 4 which is fully updated and I'm using iTunes 10.4.0.80 (although this has been a problem with previous versions as well) on Windows 7.
When I try to sync my phone to my computer it tries to install all the apps I've installed and deleted from my phone since I last synced. I've only got a 16GB phone and I tend to install and delete apps regularly, so this fills up any available space and prevents me from syncing what I wanted to sync to my phone in the first place. The check box for "automatically sync new apps" is unchecked. I can (and at the moment, I have to) go through the list and uncheck every app that iTunes has checked for me, but with over 1000 apps backed up on my iTunes this is extremely tedious, and given that iTunes runs extremely slowly on my computer it often takes me more than 4 hours to do. It is slightly quicker to uncheck and recheck sync apps, then manually add back all the apps I want to keep, but I still have to (still extremely slowly) scroll through the list to add back in the same set of apps each time. Even if I could use the phone display on the right hand side of the screen to delete the new apps it would be easier, but no matter what I do to the display, if I don't uncheck them in the list they just get added back on again anyway.
Is there a way around this or am I stuck devoting hours to syncing my phone every time I want to move stuff between my computer and my phone?

Starting when iOS 7 was released, Apple now allows downloading the last compatible version of some apps (iOS 4.2.1 and later only)
App Store: Downloading Older Versions of Apps on iOS - Apple Club
App Store: Install the latest compatible version of an app
You first have to download the non-compatible version on your computer. Then when you try to purchase the version on your iPod you will be offered a compatible version if one exists.

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