Maybe it has already been mentioned, but why not the 70-300 f/4-5.6L IS USM?
Excellent IQ & IS comparable to the 70-200, better than the 100-400 - not quite as much range. But significantly shorter and lighter than both of the other options you listed. Could be a more practical lens out in the field.
If I had the cash, I'd use the 70-200 f/2.8 sans TC when the wide aperture is needed, and the 70-300 when more range, less weight/size was needed and aperature less important... They complement each other well.
The 100-400 I think you will always be stuck with a heavier+longer lens even if redesigned, and it doesn't differentiate itself as much from the 70-200 as the 70-300 does (aside from the controversial push-pull zoom).