Thing is the 70-200mm is a great lens at f2.8 which is something the 100-400mm can't do ever.
Meanwhile the 100-400mm MII is better at the 200-400mm range. The 70-200mm f2.8 IS L MII + 2*TC (taking it to a 140-400mm) can just get about as good as a 100-400mm MKI. The 100-400mm KII is better than the original by a long shot so in turn its far better at the long end.
Honestly I think this is more about you having to decide if what you do requires one lens more than the other; its sounding right now that you're thinking of long distance stuff and thus leaning strongly toward the 100-400mm. However other situations might push you the other way. The correct choice might even be to save money in other places and even delay the camera body update as selling either lens could set you back in some specific area.