This is the most annoying thing about metacity.  It is counter to years of
use and standard practice.  Here's an(other) example of when this sucks.

Imagine you are using a database query tool (eg. tora) and you have a lot
of data to view.  The app is maximized.  Now you want to bring up a
calculator and total up a few things that are the results of some adhoc
query.  Suppose that these items are not 'on the same screen' but you must
do some scrolling to access the items that need to be totalled.  

You bring up a calculator, then scroll to the first item.  The calculator
is now behind.  You hit alt-tab.  You type in the number.  Repeat. 
Clicking the scroll bar (or a link on a web page) should not raise the
browser.  If it does, it's a bug.

This is really annoying and happens to me almost on a daily basis.  Even
just now while entering this bug I encountered it.  I wanted to find the
bug # that this is a duplicate of (see, I'm a nice guy, I'm even giving you
the duplicate bug).  I found it, and wanted to paste it into a temporary
buffer (since cut-and-paste is so flaky, that's a whole other issue).  Put
simply the middle-click into some other window raised it.  Uggh.

I understand that this is a duplicate of bug 86108, but I just think the
developers should just ADD THE DAMN FEATURE already.  Please?

I've never heard of a situation where so many users complain about
legitimate problem, submit patches, agree on a simple effective solution
and are told by the developers:

<paraphrase> we would rather solve this with a collection of complex
special cases, none of which address the general problem you are bringing
up.  We changed the behavior because of arguments made by someone.  We
don't have those arguments now, nor any arguments about why the behavior
you want shouldn't be the DEFAULT behavior.  But tough luck, we are closing
the bug.
</paraphrase>


By the way, if you decide to keep the existing behavior, then keyboard
activity should also auto-raise the window.  Why descriminate?  If using
the mouse raises the window, then using the keyboard should raise it. 
Otherwise the behavior is really just inconsistent.