I'll try to keep my post unbiased and stick to the facts. All of this information is currently based on the spec sheets and what we know from hands on usage of current DSLRs. The 6D has yet to have any public reviews, so any discussion of the AF or ISO performance is not yet based on lab tests of a production copy of the body. This is important to understand, as it is possible that either spec may not hold up to its perceived improvement.
Keep in mind that these cameras were announced four years apart from one another. That is quite a time span, so some of the technology has improved, and even though the 5D series is positioned slightly above the 6D series some of the technological advancements have made their way into the 6D line.
The biggest of these advancements will likely be seen in the progression from the Digic 4 to Digic 5+ processor. With this you get a native ISO range on the 6D that adds 12,800 and 25,600. You also get the expanded options of 50, 51,200 and 102,400. The new processor can also attribute to faster frame rates, higher burst capacity, and improved performance at the same ISO.
- Weight: The 6D is .17lb (77g) lighter
- Size: The 6D is about 13% smaller
- GPS: The 6D has it built in, 5D MKII requires additional hardware
- WiFi: The 6D has it built in, 5D MKII requires additonal hardware(WFT-E4 IIA $675)
- Framerate: The 6D is slightly faster at 4.5fps, the 5D MKII is 3.9fps
- Shutter Speed(Max): The 5D MKII is 1/8000 sec, the 6D is 1/4000 sec
- Viewfinder: The 5D MKII has 98% coverage, the 6D has 97% coverage
- LCD Display: The 6D has a 3" 1,040,000px display, the 5D MKII has a 3" 920,000px display
- UI: Updated UI is newer on the 6D
- Autofocus: The 6D has 11 focus points(single center cross type), the 5D MKII has 9 user focus points, 6 assist(single center cross type)
- Resolution: The 5D MKII has a slightly higher resolution of 5616 × 3744, the 6D has 5472 x 3648
- Metering: The 6D has a 63 zone system, the 5D MKII has a 35 zone system
- Sync Speed: The 5D MKII has a flash sync speed max of 1/200sec, the 6D has a max of 1/180sec
- Shutter Life: The 5D MKII has a shutter life of 150,000 actuations, the 6D is 100,000
- Metering: The 6D has a range of -3 - 20EV, the 5D MKII is 1 - 20EV or .5 - 20EV(I've read conflicting reports)
- Memory: The 6D uses SD/SDHC/SDXC/UHS-I, the 5D MKII uses Compact Flash, UDMA
- Scene Modes: The 6D has scene modes available, the 5D MKII does not
- Sensor Size: The 5D MKII sensor is 24x36mm, the 6D is 23.9x35.8(microscopically smaller)
- Sealing: The 5D MKII is dust and water resistant, 6D is splash and dust resistant
- Frame: The 5D MKII is completely magnesium alloy, the 6D is made of magnesium alloy with the exception of the top plate which is polycarbonate(allows for the WiFi)
Keep in mind, at least two separate upgrade paths exist. If you already have a 5D MKII, and are looking to switch to the 6D, the differences are very small. If you have a Rebel line DSLR, the differences will be much more significant for example.
As of 10/25/12 - The Canon 5D MKII body has an MSRP of $1699, and the 6D is at $2099. That is a $400 difference. Obviously the 6D is not currently available, with a planned release date of December 2012. The 5D MKII may or may not be discontinued at that time, and the price may or may not go down.
I'll leave it up to you to draw conclusions on the above, I don't want to push you toward either solution - as price, availability, and current equipment make this a personal choice.