Owning both currently, there isn't any real difference in optical quality between them that I can see (on 7D) and I wouldn't worry about that. I'll happily use either at any focal length wide open, when the only time I stop down is if I need more depth of field.
It was mentioned the difference between 200-300mm didn't appear great, that could well be the case if tested at relatively close focus. The 70-300L does suffer from noticeable focal length shrinkage when close focusing, where I can't say I noticed any on the 100-400L.
Aside from that, the differences are pretty much well known, with the 70-300L having the newer IS system, better sealing, and being much smaller and lighter. The 100-400L gets you the extra reach, and love it or hate it, you have the pump action zoom. If you put a gun to my head and say I could only have one of these, I'd pick the 100-400L without hesitation.