It would be nice to have default preferences that the user could set up (under File-> Preferences, naturally) for things like sprite size, layout size, etc. That way whenever a new one of whatever is created, it's made with those preferences that the user has specified. (As alspal said in another thread, having a new layout automatically be the same size as the app resolution would be nice... perhaps a radio button to enter a user-defined size, and another for "Match Application Size")
This could extend to new apps too, for automatically setting options like resolution, sampling, scripting, default controls, and all that jazz.
I just find that I'm always changing the same things whenever I start a new app, so it'd be nice to be able to customize it.