Even I felt Xcode's window management was out of place when I started using it. Learning some keyboard shortcuts eased the pain.

Here are some links: http://cocoasamurai.blogspot.com/2008/02/complete-xcode-keyb...

http://groups.google.com/group/des-moines-cocoaheads/browse_...

Additionally, you can script Xcode using several scripting languages. You can also write plugins for Xcode using AppleScript.