I spent a lot of time debating this very choice. I shot with a 70-200 f4L IS on my 50D for a couple of years, with and without a 1.4ii extender. Loved the IQ of the naked lens, and the lens+1.4 was still very, very good, but it always seemed too short for my needs. I eventually opted for the 100-400 and I have been very pleased so far. Technique is crucial at the longer focal lengths, but when I nail focus at 1/60-1/125 (or use a good tripod) I think the IQ is just fantastic (unless shooting over ISO 800, of course, then noise prevails).
This funny shot of a suberb starling at the Atlanta Zoo was taken from about 12 feet at 400mm/f6.3 at 1/60 hand-held (200ISO) and minimally processed in Lightroom (basically just cut a portrait out of a landscape, so it's only cropped horizontally a bit, and bumped up clarity and optimized exposure). At 100% there's great detail in the feathers and the bokeh is really nice. I find this lens sharp wide open but it's hard to get the right DOF for many subjects so I bump to 6.3-8 more for DOF than lens performance. Even on this starling I'd like more of the beak in focus at 6.3, but it still works.
I was sorely tempted by the close focusing of the 300 f4 IS and AF of the 400 f5.6, but I wanted that 100-300 range too much. I think this is really splitting hairs and comes down to minor preferences until you get to options like the 300 f2.8L which is in another league (and price orbit).