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I have the 70-200 f2.8 IS and the 100-400.
I use the 70-200 more than the 100-400 but I have a bigger prime telephoto for the longer end so use that more.
The 100-400 is a great lens, like all long zooms it suffers with image quality right at the 400mm lens and can be quite soft. The image stabiliser is not all it's cracked up to be and you still need quite fast shutter speeds to get the best from it, especially above 300mm.
It's a push-pull zoom rather than twist like most lenses, some people blame internal dust problems on this but I can't say I've noticed any problems with it.
Even with IS I think you'll need more light with the 100-400 than the 70-200 as it's 5.6 at the longer end.
If I could have one lens only I'd take the 2.8 70-200 above both your choices, if it was a choice between the f4 and the 100-400 I'd probably go for the 100-400.
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