Sounds like some of these issues could be easily solved by setting up Behaviours properly. This is something new with Xcode 4, and allows you to configure what Xcode should do when certain events are triggered.
For example, the event for when "Run Completes" will trigger the behaviour "if no output, hide Debugger". This can be switched to always hide to solve the described problem.
I realise this doesn't solve the resizing issue, but it's a very handy indeed and makes working with panes a much better experience.
I complained about similar problems, particularly with a multi monitor setup. Then I really dug into behaviors and tore tabs off into new windows. Productivity bliss!
There's a very good video on behaviors from wwdc if I remember correctly. Go look at the session videos, it was very helpful.
Agreed, especially as Xcode 4 does a pretty outstanding job of ruining my multi-monitor setup.
The problem with any set of panes is that they almost always lack features X, Y and Z that you miss from a window manager. That's what the window manager is for, and it frustrates me that applications feel the need to implement this again and again (each in their own way, to boot).
It is time for a modern GUI to provide support for chromeless panes as first-class windows, so that you can move any pane anywhere, attached to any number of other things from any application, with any size in any arrangement (tabbed, split-pane, whatever).
For example, the event for when "Run Completes" will trigger the behaviour "if no output, hide Debugger". This can be switched to always hide to solve the described problem.
I realise this doesn't solve the resizing issue, but it's a very handy indeed and makes working with panes a much better experience.