I've had this debate a bit myself as I own the 70-200 but do a lot of wildlife work. The old 100-400 never made me happy, but I was very close to pre-ordering the 100-400. Then the 11-24 f/4 leaked and that interests me more, but I'll give you my thoughts:
70-200 f/2.8 IS II or f/4 IS are both brilliant lenses, with the f/4 being just as good, but costs much less and is much smaller & lighter. Both take the 1.4x extenders very well and are excellent for wildlife shooting. The 2.8 is also a great low light & event/sports lens, plus excellent portrait and general purpose lens. The f/4 can be used for these as well, but has less shallow DOF and needs 1 more stop. With the 2x, the f/4 AF struggles a bit more in lower light, but works. The f/2.8 takes the 2x very well, but becomes somewhat long and bulky, and isn't very pleasant ergonomically, but is still viable.
The new 100-400 looks to be extremely sharp & versatile, offering all of the above without the need to reach for extenders, with the tradeoff being less light, less shallow DOF, and bigger size/weight. Unless you need low light / action stopping ability (less critical with the newer DSLR bodies high ISO capabilities) or shallow DOF for portraits, I'd go for this lens as it's more versatile and 1 purchase vs. 2 or 3 (with the extenders).