I was thinking of user-defined, nameable modes, with a few defaults mapped to easy keybindings.
Navigation and combat would be my two...
Navigation has a ton of sensor windows and tracking the first, say, 5 closest "ships" and 1 closest "object", as well as a flight plan indicatior. very little window room actually visible.
Combat has a sensor window set up for short range, perhaps two on different axes... weapons loadout w/ammo indication and recycle time bars, and a damage display on the nearest hostile ship, with a key setup to lock on to that ship until it is destroyed or you hit the lock key again. I'd also like a window showing the last ship to damage me, or perhaps the ship that has done the most damage to me in the last 2 minutes combined.
Leave enough space for 5 or 7 setups, and have a default that you launch in (or just revert to last used), and have each one have it's own keymap too, defaulting at all the same keys for basic flight, specialty keys different... and, say, ALT-1 for mode 1, ALT-2 for mode 2...
Oh yeah, and switching to certian modes should be able to do certian things to your ship: going into combat mode should raise the shields, arm all weapons, and possibly re-route power from the engines and life support to weapons and shields (in navigation mode, basically do the opposite.)
Exploration mode I envision being basically a hybrid of the first two: weapons armed and shields up, but a bunch of navigation and scanner windows, with power set up for engines, shields and life support, and only minimal weapons: just enough that you can shoot back, but not any more than that -- if you need weapons in a hurry, they're there, but you're not wasting energy on them, and you can switch to combat mode easily enough if you need heavy weapons.
Each of these windows should be customizable too, maybe with XML for each window -- but we should include enough different useful windows that the average user doesn't have to mess with XML.
Just a note on the XML -- I feel that no user should have to edit any XML, except for the power users that want to do extreme customization -- like making thier own, complicated version of the auto-updater (target nearest ship, unless there's a hostile ship within 5000km, in which case target that one, unless it's distance from me is increasing, just as an example of something that I don't feel we should include as a default, but have the ability to create.)
Now, how will average users do basic customization? We should have a in-game graphical utility that lets users drag-n-drop components and resize them etc into a window and then have the program write out the XML. Maybe as a free download on the website, or as a seperate program bundled with the game, but it should be available somehow.
Hell, I'm not a dev, but maybe such a third-party-tool I (or anyone else) could write, and you could just provide it on your site in the community area.