Of the things you've listed there are only three things that would influence my buying decision. The swivel screen LCD on the D5000, and the menu controls, and lens selection.
I've actually considerd buying a D5000 jsut for the swivel screen. When using it with Live View, it can be a major advantage for getting shots you might not be able to get without it, especially if you're shooting Macro and Landscapes. Imagine not having to crawl around on the ground to see whether your shot is composed properly.
Secondly, most reviewers say that Nikon blows away Canon as far as ergonomics are concerned. From my experience using both a Canon and Nikon with one wheel controls, I also prefer the exposure contorls on Nikons. You're experience may be different, especially since you're used to shooting a Canon P&S. If you haven't tried this out for yourself, go to a camera shop that has both and get your hands on them. Nobody can tell you which one will work for you.
Lens selection is a biggie. Canon definitely has a larger selection of lenses, and I really don't understand Nikon's entry level AF motor strategy. This is probably Nikon's biggest weakness IMO. The lenses they do make are made very well, but they really could stand to expand their lineup a bit.
As for the other things:
Depth of Field Control -- I'm not sure what you mean by this. The Lens and aperture selection have much more impact on DoF than does the camera body. Unless you're referring to the kit lenses.
12bit vs 14bit RAW files -- I've never had trouble getting a great picture because I lacked those extra two bits of color depth.
Weight -- Not really an issue, especially when you start adding more lenses and accessories to your kit.
Faster continuous shooting -- Are you going to be shooting a lot of sports/action shots. If not then this shouldn't be a factor in the decision.
Scene modes -- If you're ready to go in shooting manual then these will quickly be ignored. The only thing you might want them for is if you plan on sharing the camera with a friend or significant other who just wants to take some snapshots. If you're the only one using the camera, and your confident you won't want to fall back on them, then don't factor them in.
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