I do agree with you that it should be an option. I must say though that this change delighted me, and is Correct (tm). ;-)
Ugh, this drives me nuts. I use focus-follows-mouse because I like being able to type into whatever window I'm pointing at, WITHOUT having to click it. It's just "less work" from a "I want to change focus to that other window"-standpoint. I don't often want to raise the window that's focused, because I like having a gaim conversation window on top of a maximized mozilla window (so I can still read the gaim window, even if I'm typing into a web form or something). BUT, sometimes I DO want to raise the window, and it's *so* much easier to be able to click anywhere than to be restricted to the title bar. I find it very annoying that I have to click in that one tiny little spot.
I don't know how to explain it, it just makes sense to me that whatever I click on ought to be given focus and raised, but whatever I point at without clicking on ought to simply be given focus. There seems to be a bug where if I move change workspaces too quickly, the newly pointed-at window won't get the focus, and clicking on it won't give it focus, I actually have to go to the trouble of moving my mouse off the window and then back on, which is very tiresom since this happens CONSTANTLY. Try it yourself: put one window on a virtual desktop, change to a different desktop, then change back by clicking on the pager (make sure you click outside of the window's outline), and then move your mouse over that window, as fast as you can. If you did it right, that window won't have focus. And clicking on it won't give it focus. Clicking on the title bar will, but that's no less annoying. For the most part, you have to move the mouse off, then back on, to give it focus.
Actually, now that I'm ranting about it anyway, GNOME really needs a "focus strictly under mouse" mode, not "focus follows mouse, poorly" as is currently implemented. There's nothing I hate more than writing an email, and having some error dialog box pop up, but disappear too quickly to read because I was typing, it stole my focus, and I pressed the space bar, which selected the default action. That dialog box, whatever it was, just did something that I might not have wanted it to do, and it might be irreversible, and I might never know what it was. That drives me nuts.
Basically, what I'm trying to say is that the window I'm pointing at should ALWAYS have focus, and the WM should never give focus to any other window, unless I point at it specifically, no matter how badly that other window may want the focus.
Does that make sense?