Honestly, I trusted Art Morris a lot more before you pointed me at his statements that the 70-200 II + 2xIII beats the 400/5.6 - I'll be reading his blog with a lot more skepticism from now on.
Art Morris' evaluations of lenses are never based on technical charts and the like. His basis for evaluating the quality of a lens is the actual results it produces in the field. Any time you ask Art about what he thinks of the quality of a lens, he'll pull out a photo of a bird he's taken with that lens, and give you a subjective evaluation of whether he believes the lens produced "professional sharpness" or not.
The technical difference between teh 100-400 vs. the 70-200+2x, as seen on TDP, is extremely small. From what I have seen when comparing the 70-200+2x III @ 400mm on TDP, the 70-200 actually performs just a smidge better center and mid frame than the 100-400. The corners perform worse, with a greater amount of CA...however given that one usually crops bird photos, center and midframe are really what matter anyway. I do not believe the differences could really be seen either way in any real-world application, with the exception of center frame, where I think the 70-200 does do slightly better...even with the 2x TC.
As for why I am keeping the 100-400, besides that slight edge in sharpness, the collapsed length when mounted is shorter (packs better), the balance is better, and the push-pull is faster to operate. When the 100-400 replacement comes along, you can bet it'll trounce the 70-200 II + 2xIII for IQ.
I totally agree, any new 100-400 will probably trounce any comparable lens that came before it. Personally, I'm a fan of the push/pull...if Canon uses a ring-based zoom approach, it'll be a hard sell on me.
To the OP, having JUST recently been through such an evaluation myself, I'll offer that I chose the 600mm f/4 L II in the end. I considered the 300/2.8 L II, 400/2.8 L II, and 600/4 L II. I do birds and wildlife, primarily birds, and there is just no denying the benefit of reach for birds. I rarely photograph them without the 1.4x TC, and with the 5D III next on my list of things to buy, I highly doubt I'll photograph many birds with anything less than 1200mm.
I think 600mm is a nice focal length for wildlife...it not only gives you reach enough to stay at a comfortable, safe distance when you need to be (i.e. rut season), but it keeps a thin depth of field and nicely blurs backgrounds. Long run, having rented these lenses in the past, I think the 300/2.8 L II is a better wildlife lens than the 400/2.8. You have a good range of versatility with TCs, but particularly the 300mm focal length which is ideal for wildlife you can get close to, and the ultra fast aperture that helps in the dimmer evening or early morning light when a lot of wildlife is up and about. The weight of the 300/2.8 is also superb for carrying around for a while. I wouldn't go so far as to say you could hand-hold the 300/2.8 "all day", but several hours for sure. If you needed more reach, you can always slap on the 2x TC III for 600mm, which is about as long as I think anyone would really want to go for wildlife.