The one big downside to Capture NX2 is that for some people (including me) it's terrifyingly slow. While I agree that Nikon's software should always have an advantage over a 3rd party's decoding capabilities, I never found LR2 or Aperture lacking to such a great degree that I would feel compelled to buy NX2 and use it.
Regarding RAW vs. JPEG, if you have a capable camera (which the D60 is), you'll want to do your work justice by shooting RAW. The true test would be: if you have a big enough memory card, try shooting RAW+JPEG sidecar (every time you press the shutter, you get one RAW and one JPEG image that's been converted by your camera). Open up either Aperture or LR2 and start playing around with your pictures. Unless you NAIL the shot, you may find yourself wanting to change exposure values, sharpness, color/white balance, etc. You can do this very easily with a RAW image, but you won't have the same amount of flexibility with a JPEG, since your camera already "developed" it for you. You can still edit those values with iPhoto, but its range/utility is much more limited.
Regarding iPhoto vs. A2/LR2, I used iPhoto for a long time, so I understand your attachment to it. A2/LR2 can't sync with your iPhone/iPod/ATV (as far as I know), and iPhoto can produce some nice books, etc. I think that's where iPhoto's advantages over A2/LR2 end. The pro programs not only are able to manage your workflow/database better (lean towards A2 here), but are also much stronger editors and developers of your photos (lean slightly towards LR2 here). If you ever want to try HDR photography, start shooting exclusively in RAW, do more than basic edits, or manage a library of more than a few thousand images... you'll be glad you switched.
Don't take this that you can't/shouldn't use iPhoto at all. A2 can interface well with iPhoto - LR2 can't do it as easily, but it can still be done.
My $0.02.