Upload & Sell: Off
On a full frame, the prime will have better corners. in addition, the prime has slightly better color and contrast at 5.6. center sharpness is very close in sharp copies of both. Keep in mind, that primes are usually easier to manufacture, and less prone to qc issues. with the focus limiter locked, the 100-400 locks and tracks well, well enough for BIF. however, the 400 is still a bit faster. at 400mm, the subject is likely far enough from you that the 400 will have no problem tracking. but if the subject is very close and moving towards you (in which case you would not be shooting at 400 anyway) the prime will have a definite advantage.
The MFD on the zoom is much closer, at 1.2M (I think) while the prime is 6 m. The IS on the zoom sucks by todays standards, and honestly is barely good for 2. thats compared to a true 4 stop IS that I get out of the new 70-200 2.8 II. the prime is lighter and more maneuvarable, and cheaper. If you know for sure, you will be happy shooting at 400, and you are using a monopod, or faster than 1/800 sec on a crop sensor, then go with the prime. I also find the IS useful for stablizing the subject in the view finder, and I often acquire target at 200mm, and then rapidly zoom to 400. just practical considerations.
couple of shots, and one showing off the mfd