Between the 300 F4 L IS, 400 5.6 L, and 100-400, I'd take the primes. Even the 300 with Canon TC is sharper than the 100-400 in my experience (as well as WCastleman and Photozone's).
The 100-400 has nice versatility, but so does a Canon S3.
I did choose a prime - the 300mm f/2.8mm II to get a huge stonking increase in performance not a tiny quantum, if any, with the antique ones. And I travel with an SX50 because it is versatile and fits in my briefcase. But, I want a really sharp 100-400 zoom with modern AF and IS to go with my Canon body for those occasions when zooming is needed and when I don't want to lug the big white primes.
5D IV, 5DS R, 7D II, EOS-M, Powershot G3 X, 400mm DO II, 300/2.8 II, 1.4xTC III, 2xTC III, EF 1.8 STM, EF 70-200/4 IS, EF 24-105, 15-85, 100-400 II, Sigma 10-20, Sigma 150-600mm C, EOS-M5 15-45, f/2 22, 11-22, Samyang 8mm f/2.8 fisheye