The shame about this complaint is that there were two features in NEXTSTEP that partially addressed the issue, as well as a full blown fix for the determined. And Apple, in it's "wisdom" decided to nuke them all as part of their "kill the handiest features in NEXTSTEP" campaign.
First, the NEXTSTEP Terminal application had a preferences option called "steal keys" that would make all terminal windows become move to focus instead of click to focus. As long as the mouse was over the window, typing would go into the Terminal window.
This was especially handy for controlling command line debuggers when working on a GUI app. Sometimes you don't want to switch out of the app because it disturbs what you're trying to debug.
If Apple would bring that feature back to Terminal, it would cover many of the cases where people want move to focus, without disturbing the GUI consistency for the non-power user. (How many grandmas are going to turn on an obscure preference in an app they probably never run?) Since it seems most people who want move to focus are heavy Terminal users anyway, this would be one small bone Apple could throw their way.
Under NEXTSTEP, back when we had Display Postscript, there was even a super short hack to the windowserver's PostScript code (only a few lines) that would actually change the whole system to move to focus. Everything, not just Terminal. You didn't have to be terribly adventurous to install it, but now that we have Quartz, instead of DPS, such a hack is sadly no longer possible (at least, nowhere near as easy -- the window server on NEXTSTEP was plain text interpreted PostScript, open and ripe for hacking).
The other really nice feature that NEXTSTEP had was with special window ordering keystrokes. You could use the command (Apple) key in conjunction with the up and down arrows to cycle through the windows (bring them forward one by one) without changing which window was focused. You can't imagine how handy this can be!
Even more handy was the ability to command click a window's title bar to send it to the back, again without changing focus. So you could get a particular window to be focused, send it to the back, and keep typing while looking at what's in the other windows. Again, very handy, and a shame we lost it!
What kills me is that this stuff was all optional, and not likely to be found by the casual user. So having it there hurts nobody, but does offer handy features to the power users. Having things that the wouldn't confuse the normal user simply because they aren't going to use them. So why on earth did Apple feel it had take out the option? Do they not realize that some of us find these sorts of features to be remarkably useful?
Of course, until more people request these features, they won't be put back in. So if you like these sort of nice touches, pester Apple to put the options back in. I don't care if they're even disabled by default, as long as there's a way I can turn them on. But I would really like to have the options back!