Sometimes (actually pretty often) it is necessary to alter a pattern size for one single object. So you go to Appearance -> Fill -> Effects -> Distort and Transform -> Transform and there you have checkboxes to chose whether to transform object or pattern or both and that is great.
But once you have done this (for one single object) this setting changes the general Option under Preferences->General and this setting affects the entire app, not this file only and you must change it back each time. And that is not that great.