Righto, I've found a solution of sorts.
Stop the phone from syncing apps in iTunes. Sync the phone but cancel the backup. This should remove all apps from the phone. This is what you want.
Then right click the phone and Reset Warnings and then Disagree sbout sending crash reports to Apple - takes ages extra if this is on.
Now sync, and the back up should be rapido.
Now add apps a couple at a time, then back up. Do this unroll all your apps are on.
Finally NEVER update apps over 3g or Wifi, always do it via iTunes. Solved my issues for now.