To summarize I believe you are proposing the following. Please advise if there is any other details I missed.
I would also like to hear what issues other folks may see with this (but didn't want to confuse things by adding my comments/concerns).
1) Add Configure pulldown menu
2a) Move Window > Preferences to Configure > Preferences
2b) Move Perspective > Customize to Configure > Perspective
3a) Configure menu would allow global preference settings to be added to it.
These settings woudl also be in the preferences dialog (available from
Configure > Preferences) .
3b) Configure menu would allow perspective centric settings to be added to it.
For example Configure > Java which would open the preference dialog
(same as Configure > Preferences) except it would select the java page.
4) The preferences dialog should go to the previous page (i.e. favorite) when it
opens, and if needed start the plugin for that page.