Flashes are a good thing, but you can't always use them.
On the other hand, there are things you can do with the flash that you can't do with an f2.8 lens. It's a very difficult choice.
You will eventually probably want a flash (maybe not one as powerful as the 580EX) which makes it even harder.
One of the advantages of the 70-200 f2.8 is that when you want something within that range, you get f2.8. You don't get that with the 100-400. And the 70-200 is a much better lens between 100-200 than the 100-400 is (and it has the lower f-stop.) But is the 70-200+2xTC better than the 100-400? I don't know. Probably not, but honestly I don't know. Plus, if you suddently need the longer focal length, you have to stop, get out the TC, put it on... and probably miss the photo.
This is one of those difficult choices. If you really think you'll use the 100-200 range of the lens more, then the 70-200 is a really great lens. But if you think you'll need the longer end more... then the choice becomes more difficult.