The current 400/5.6 prime is already optically better than the 70-200/2.8L IS II + 2x TC, and the bare zoom is better than the bare 200/2.8 prime.
Which is why there's no need for a 400/5.6L IS if the 100-400L is replaced. The version II will very likely be better optically than the current 400/5.6L, have IS, focus just as well if not better, have better MFD and be able to zoom out as a bonus. Sure it will be expensive but who thinks a 400/5.6L II will come in under $2,500? The zoom will sell more and therefore benefit more from the cost reduction you get from volume production.
I don't disagree, at least from the consumer's perspective. The zoom would be more popular. As I stated, from a business perspective, the current 100-400L sells well...very well! By some reports, Canon sells more 100-400's than 70-300L's, despite the latter being newer and sharper. If Canon has both a new 100-400 and a 400/5.6 designed and production-ready, it might make business sense to release the new prime first, wait a couple of years, then release the new zoom.
I'm an old man...I don't know if I can wait that long