what about the larger more detailed viewfinder and DOF control?
It's not
that much larger, and they pretty much display the same information in there anyway. DOF control? Lenses are lenses are lenses. The 18-55 at f/8 will act exactly the same on the D5000 as it will a D90, or even the D2x. Now DOF preview, that might be what you meant, but I don't even use that on my D700, and I would say that few actual photographers use DOF preview anymore. DOF preview now is the LCD, this isn't film anymore. Take a shot, review, zoom in at 100%, if what you want is sharp, it's sharp, if not, it's not. you can't see those subtle differences through the tiny finders of 35mm.
and multiple physical controls instead of menu based settings.
Regardless if you're shooting a D90, or a D5000, changing things like ISO are still a two handed operation, and there's almost no menu flipping to change things like the ISO or WB on the 5000 or D40. Just hit the info button twice and you're there, it's fast, it's easy. If you're going through the menu>shooting menu>White Balance (etc..) then it's user error. Granted it's not the hold down ISO and rotate a dial fast as the D90, but it's really not
that tedious.
those things plus the motor for AF... there is no reason to even consider the D5000 over the D90. maybe if you could find the D5000 for about $350, but by that time you'll be able to find the D90 for $400
Uhh, price? size? easier video? identical image quality? similar AF system? similar frame rate? The 5000 is $850 with a lens, the D90 is $1000
body only. like I said earlier, the only two things the D90 substantially offer for
my uses is a screwdriver for my 80-200, and a commander for the pop up flash. Otherwise, the D5000 is pretty much just as capable.
It's like the D700 and the D3. Why would anyone spend a $2000 premium for another CF slot, integrated grip, one more fps, and more klunk and weight unless they know they'll use those all the time?
Personally, i'd use the screwdriver on the D90 all the time because of my 80-200, and I have 3 SB600's, so i'd need the commander too. I could justify the D90. However, if I didn't have those things, then I wouldn't pay extra money for "fluff".