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Originally Posted by CourtJester
-Get to a store and hold each camera, ergonomics is important
-Research lenses as well (I was planning on buying the body only anyway), but this is a big consideration
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I'd actually put lenses before ergonomics, but that's my personal taste. I can deal with irritating user interface issues: I work on UNIX, OSX, and Windows in my professional life.

My logic is that only two things "touch" the light: the sensor and the glass. Everything else is gravy.
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-Sounds like the way Canons change ISO settings are the much preferred method, sans menu navigation
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This is where the hands-on can help you. Also, from what I've read, Nikon's auto-ISO is more intelligently handled than on the Canon side (i.e., some models have an ability to set an upper bound to the iso), so you may need to change the ISO less frequently.
Ok, going back to your original post, here's how I rate the importance to me of each of your points on a scale of 1 (not an issue) to 10 (dealbreaker):
The LCD specs and I don't care for the swiveling screen of the Nikon
5. You work with the LCD all the time.
Depth of field control
If you mean the A-DEP mode, 0. DEP used to work just fine back on the film cameras, but Canon made A-DEP harder to use properly and it's very easy to get it wrong. I've never used it, but then, I don't do a lot of group shots. There's a reason A-DEP is not on the 1-series cameras. I prefer using a DoF preview button (which, sadly, the D5000 doesn't have) or doing hyperfocal distance the old-fashioned way.
14 bit RAW vs 12 bit
2. Yes, there's a difference, but
not as much as you might think. Past a certain point, expanding the color space just gets you less and less.
All lenses can AF & possibilities seem greater to expand into better lenses (price)
8. But I'm mostly a prime shooter. If you plan to shoot primarily with zooms, this would be more like a 4. The majority of Nikon's zooms are AF-S, so they will autofocus. And if the two lenses spec out similarly, the costs are relatively close. Where you'll find cheaper lenses on the Canon side is when they offer a lower-speced alternative. Say, a 70-200 f/4 as well as a 70-200 f/2.8.
But that's
new lenses. Nikon also has the ability to mount old manual-focus lenses directly onto the camera. You'll lose metering, autofocus, and the ability to shot in any modes but full manual and aperture-priority, but you have compatibility back to the '70s on used lenses. If you go up-tier, with a D80/D90, you'll get metering back. And if you go up to a D200/D300/D300s, you'll have the ability to set up some EXIF information for the lenses, too. And old manual focus lenses often go for bargain prices from those who upgraded their glass to autofocus.
Canon, otoh, can only directly mount EOS lenses from 1985 forwards. The old manual-focus FD/FL lenses will not work and cannot be adapted.
With adapter rings, EOS can use manual focus lenses in the Nikon F, Pentax K, Contax-Yashica (Zeiss), Leica-R, Olympus OM, and M42 mounts, but you will lose autofocus and can only shoot in M and Av. You do, however, have stop-down metering capability. And, of course, your EXIF is munged. Still, small price to pay to mount cheap Zeiss and Leica lenses, imho.
MUCH easier to change settings like ISO & aperture w/o going through menus
3. As I said, I eventually just learn workarounds for UI irritations.
Lighter in weight
7. But I suffer from RSI. Most folks prefer a heavier camera.
Faster continuous shooting
2. I shot birds in flight with 3fps on my XT. I now shoot them with 6fps on my 50D, and that's about the only time I find having a higher frame rate helps, and there are times it's made me accidentally take frames I didn't want. If you can't decide your moment, a higher frame rate still isn't gonna snag it for you: you just get more shots of the wrong moment.
Advanced scene modes (although I plan to shoot mostly in manual)
0. I never use scene modes.