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$700 in your pocket. The 5D costs $3,300 vs. $4,000 for the 1D Mk-II N.
Deeper buffers: 60 JPG vs. 23. I've never needed more than a 20 frame buffer anyway.
Spot meter. I've never used this.
Much, much lighter: 31.5 ounces versus 54 ounces, including batteries! The 1D Mk-II N is much heavier, and it's batteries are heavier still.
Superior battery technology: Li-ion vs. NiMH of 1D Mk-II N. NiMH usually want to be babied to retain performance and weigh a ton. Li-Ion don't require any cycling or reconditioning as NiMH do. NiMH are used in the professional 1D Mk-II N because NiMH can belt out more instantaneous power to support the 1D Mk-II N's scary 8.5 FPS shooting rate versus the 5D's pedestrian 3 FPS.
Durability. I have yet to do a head-to-head, however the 1D Mk-II N is built to Canon's top durability and weather standards and the 5D seems similar to a 20D. This is a huge issue and the main reason, in my mind, to pay $3,500 for a camera versus $1,200.
Frame Rate: Only amateur 3 FPS versus 8.5 FPS.
No sound memo. No big deal.
Sensor Size: The 5D has a slightly larger sensor. Pixel pitch is the same 8.2 microns in each camera. The 5D will always have wider angles, an advantage for wide angles and a disadvantage for telephoto shots. Likewise at the same angle of view and f/stop the 5D will have very slightly less depth of field. Neither the 5D nor 1D Mk II N can use the 10 - 22 mm lens. Telephoto angles of view are also always wider on the 5D whether you like it or not. This is personal preference.
Viewfinder: I believe the 5D has a typically dinky viewfinder while the 1D Mk-II N has a brilliant large one. I find crappy viewfinders actually help photography. You have to work harder to make an image look good in a crappy viewfinder. The image needs to be composed strongly enough to look good as a small image. If it can do that then you've got a good image. With a huge viewfinder anything looks good. The problem is that when printed the image no longer looks so good. Thus I'm not concerned with the quality of the viewfinder.
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