Note that although the new "over the air" option now exists, iTunes will alert you to update your phone when you plug it in, and then prompt to download the 700MB firmware. You then have to intuitively think "ooh, hang on, isn't there an OTA smaller option?", cancel it, and search for the software update in the settings of the iPhone (46MB). From what I can tell, there's no auto-notification on the phone itself.
a) why couldn't the phone alert you instead of iTunes allowing you to go straight to the OTA option and b) why can't iTunes manage to recognise only the 46MB download is required?