yeah i've been finding this a bit of a chore too, i think only prompting if the window has been altered is a fair comprimise (and perhaps bringing up "do you want to save?" instead of do you want to close?)
also on my pretty please pd request list is a "define shortcut keys mode" - i prefer just being able to press ctl-1 for an object rather than ctl-shift-1 - don't want to start a flame war on the merits of either, thought having a preferences file for individual pd wranglers to choose would be a way to keep everyone happy
and today i got to thinking that i'd like some kind of easy record mode... just to be able to press a key and have the current sounds playing recorded to file until i press the key again... and the audio files incrementally named automatically so that it requires no user intervention at the point of finding stuff, and no need to patch in a recording object.. this sounds like an abstraction that i'm fixing to make but i thought it would be a great feature to have built into the app.
all the best
adam