I love my 70-200 IS 2.8 with Canon's x2 TC II.
But, most of my photos are shot at the 70-200 range (the money shots, if you will), and the TC provides mostly a great reaching capability, at the cost of 2 f stops and a bit of sharpness. It is softer than the regular L quality, but not soft enough to make it a bad choice. Plus for News and Press, I am better off sporting the TC in a pocket, than carrying a whole other lens altogether.
70-200 + TC = f5.6
So if you are bird watching, and you already know 400mm is what you want, I would go with the 5.6 400mm L. It will retain the most quality out of the image. And none of the kinks you have to put up with the 100-400L.
If you are not sure, the 70-200 IS with the TC may be a better solution, as it gives you a much wider range of use (70mm-400mm) with either L Quality, or still very good quality.
Just my .02 cents, and I'd love to hear which one you choose in the end, and specially how it works out for you.