I rather see a 400/5.6 with IS than a 100-400. Why? Cause you'll be shooting at 400 almost all the time!
The recently released zooms (70-200, 24-70 based on MTF) are beating older primes in the same range. If the new 100-400 follows suit, there likely will not be a lot of IQ difference. So...I see big advantages in the zoom: 1) when you want to shoot shorter than 400mm (air shows, birds flying toward you) and 2) much shorter retracted length. For me, #2 is a huge advantage of the current 100-400mm over the 400/5.6 prime.
Assuming a prime and zoom of similar focal length and f-number are released the same year the prime will have the price, weight, IQ and technology advantage.
Not to mention today's 400/5.6 older than the 100-400 being replaced.
Canon prices are high for a number of reasons. Strong yen, high demand and year of release being some of them. Street prices on lenses happens between 6-9 months after release depending on how popular the lens is.